SVMCrossVal.git

searchlight ready. missing nifti-image-write support. added timing to FBS
Parent 7614718
Christoph Budziszewski

Christoph Budziszewski commited on 2009-03-30 17:54:25
Zeige 40 geänderte Dateien mit 11578 Einfügungen und 27 Löschungen. 

git-svn-id: https://svn.discofish.de/MATLAB/spmtoolbox/SVMCrossVal@167 83ab2cfd-5345-466c-8aeb-2b2739fb922d
NIFTI_20090325/affine.m
Zeige Datei @ 87b08fd
... ... 
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+%  Using 2D or 3D affine matrix to rotate, translate, scale, reflect and
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+%  shear a 2D image or 3D volume. 2D image is represented by a 2D matrix,
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+%  3D volume is represented by a 3D matrix, and data type can be real
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+%  integer or floating-point.
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+%
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+%  You may notice that MATLAB has a function called 'imtransform.m' for
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+%  2D spatial transformation. However, keep in mind that 'imtransform.m'
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+%  assumes y for the 1st dimension, and x for the 2nd dimension. They are
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+%  equivalent otherwise.
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+%
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+%  In addition, if you adjust the 'new_elem_size' parameter, this 'affine.m'
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+%  is equivalent to 'interp2.m' for 2D image, and equivalent to 'interp3.m'
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+%  for 3D volume.
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+%
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+%  Usage: [new_img new_M] = ...
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+%	affine(old_img, old_M, [new_elem_size], [verbose], [bg], [method]);
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+%
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+%  old_img  -	original 2D image or 3D volume. We assume x for the 1st
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+%		dimension, y for the 2nd dimension, and z for the 3rd
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+%		dimension.
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+%
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+%  old_M  -	a 3x3 2D affine matrix for 2D image, or a 4x4 3D affine
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+%		matrix for 3D volume. We assume x for the 1st dimension,
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+%		y for the 2nd dimension, and z for the 3rd dimension.
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+%
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+%  new_elem_size (optional)  -  size of voxel along x y z direction for
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+%		a transformed 3D volume, or size of pixel along x y for
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+%		a transformed 2D image. We assume x for the 1st dimension
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+%		y for the 2nd dimension, and z for the 3rd dimension.
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+%		'new_elem_size' is 1 if it is default or empty.
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+%
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+%		You can increase its value to decrease the resampling rate,
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+%		and make the 2D image or 3D volume more coarse. It works
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+%		just like 'interp3'.
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+%
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+%  verbose (optional) - 1, 0
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+%		1:  show transforming progress in percentage
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+%		2:  progress will not be displayed
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+%		'verbose' is 1 if it is default or empty.
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+%
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+%  bg (optional)  -	background voxel intensity in any extra corner that
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+%		is caused by the interpolation. 0 in most cases. If it is
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+%		default or empty, 'bg' will be the average of two corner
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+%		voxel intensities in original data.
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+%
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+%  method (optional)  -	1, 2, or 3
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+%		1:  for Trilinear interpolation
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+%		2:  for Nearest Neighbor interpolation
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+%		3:  for Fischer's Bresenham interpolation
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+%		'method' is 1 if it is default or empty.
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+%
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+%  new_img  -	transformed 2D image or 3D volume
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+%
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+%  new_M  -	transformed affine matrix
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+%
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+%  Example 1 (3D rotation):
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+%	load mri.mat;   old_img = double(squeeze(D));
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+%	old_M = [0.88 0.5 3 -90; -0.5 0.88 3 -126; 0 0 2 -72; 0 0 0 1];
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+%	new_img = affine(old_img, old_M, 2);
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+%	[x y z] = meshgrid(1:128,1:128,1:27);
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+%	sz = size(new_img);
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+%	[x1 y1 z1] = meshgrid(1:sz(2),1:sz(1),1:sz(3));
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+%	figure; slice(x, y, z, old_img, 64, 64, 13.5);
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+%	shading flat; colormap(map); view(-66, 66);
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+%	figure; slice(x1, y1, z1, new_img, sz(1)/2, sz(2)/2, sz(3)/2);
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+%	shading flat; colormap(map); view(-66, 66);
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+%
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+%  Example 2 (2D interpolation):
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+%	load mri.mat;   old_img=D(:,:,1,13)';
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+%	old_M = [1 0 0; 0 1 0; 0 0 1];
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+%	new_img = affine(old_img, old_M, [.2 .4]);
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+%	figure; image(old_img); colormap(map);
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+%	figure; image(new_img); colormap(map);
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+%
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+%  This program is inspired by:
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+%  SPM5 Software from Wellcome Trust Centre for Neuroimaging
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+%	http://www.fil.ion.ucl.ac.uk/spm/software
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+%  Fischer, J., A. del Rio (2004). A Fast Method for Applying Rigid
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+%	Transformations to Volume Data, WSCG2004 Conference.
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+%	http://wscg.zcu.cz/wscg2004/Papers_2004_Short/M19.pdf
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+%
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+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
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+%
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+function [new_img, new_M] = affine(old_img, old_M, new_elem_size, verbose, bg, method)
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+
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+   if ~exist('old_img','var') | ~exist('old_M','var')
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+      error('Usage: [new_img new_M] = affine(old_img, old_M, [new_elem_size], [verbose], [bg], [method]);');
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+   end
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+
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+   if ndims(old_img) == 3
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+      if ~isequal(size(old_M),[4 4])
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+         error('old_M should be a 4x4 affine matrix for 3D volume.');
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+      end
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+   elseif ndims(old_img) == 2
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+      if ~isequal(size(old_M),[3 3])
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+         error('old_M should be a 3x3 affine matrix for 2D image.');
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+      end
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+   else
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+      error('old_img should be either 2D image or 3D volume.');
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+   end
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+
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+   if ~exist('new_elem_size','var') | isempty(new_elem_size)
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+      new_elem_size = [1 1 1];
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+   elseif length(new_elem_size) < 2
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+      new_elem_size = new_elem_size(1)*ones(1,3);
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+   elseif length(new_elem_size) < 3
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+      new_elem_size = [new_elem_size(:); 1]';
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+   end
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+
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+   if ~exist('method','var') | isempty(method)
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+      method = 1;
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+   elseif ~exist('bresenham_line3d.m','file') & method == 3
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+      error([char(10) char(10) 'Please download 3D Bresenham''s line generation program from:' char(10) char(10) 'http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=21057' char(10) char(10) 'to test Fischer''s Bresenham interpolation method.' char(10) char(10)]);
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+   end
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+
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+   %  Make compatible to MATLAB earlier than version 7 (R14), which
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+   %  can only perform arithmetic on double data type
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+   %
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+   old_img = double(old_img);
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+   old_dim = size(old_img);
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+
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+   if ~exist('bg','var') | isempty(bg)
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+      bg = mean([old_img(1) old_img(end)]);
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+   end
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+
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+   if ~exist('verbose','var') | isempty(verbose)
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+      verbose = 1;
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+   end
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+
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+   if ndims(old_img) == 2
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+      old_dim(3) = 1;
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+      old_M = old_M(:, [1 2 3 3]);
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+      old_M = old_M([1 2 3 3], :);
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+      old_M(3,:) = [0 0 1 0];
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+      old_M(:,3) = [0 0 1 0]';
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+   end
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+
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+   %  Vertices of img in voxel
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+   %
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+   XYZvox = [	1		1		1
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+		1		1		old_dim(3)
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+		1		old_dim(2)	1
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+		1		old_dim(2)	old_dim(3)
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+		old_dim(1)	1		1
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+		old_dim(1)	1		old_dim(3)
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+		old_dim(1)	old_dim(2)	1
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+		old_dim(1)	old_dim(2)	old_dim(3)   ]';
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+
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+   old_R = old_M(1:3,1:3);
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+   old_T = old_M(1:3,4);
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+
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+   %  Vertices of img in millimeter
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+   %
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+   XYZmm = old_R*(XYZvox-1) + repmat(old_T, [1, 8]);
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+
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+   %  Make scale of new_M according to new_elem_size
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+   %
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+   new_M = diag([new_elem_size 1]);
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+
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+   %  Make translation so minimum vertex is moved to [1,1,1]
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+   %
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+   new_M(1:3,4) = round( min(XYZmm,[],2) );
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+
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+   %  New dimensions will be the maximum vertices in XYZ direction (dim_vox)
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+   %  i.e. compute   dim_vox   via   dim_mm = R*(dim_vox-1)+T
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+   %  where, dim_mm = round(max(XYZmm,[],2));
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+   %
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+   new_dim = ceil(new_M(1:3,1:3) \ ( round(max(XYZmm,[],2))-new_M(1:3,4) )+1)';
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+
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+   %  Initialize new_img with new_dim
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+   %
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+   new_img = zeros(new_dim(1:3));
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+
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+   %  Mask out any changes from Z axis of transformed volume, since we
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+   %  will traverse it voxel by voxel below. We will only apply unit
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+   %  increment of mask_Z(3,4) to simulate the cursor movement
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+   %
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+   %  i.e. we will use   mask_Z * new_XYZvox   to replace   new_XYZvox
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+   %
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+   mask_Z = diag(ones(1,4));
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+   mask_Z(3,3) = 0;
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+
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+   %  It will be easier to do the interpolation if we invert the process
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+   %  by not traversing the original volume. Instead, we traverse the
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+   %  transformed volume, and backproject each voxel in the transformed
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+   %  volume back into the original volume. If the backprojected voxel
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+   %  in original volume is within its boundary, the intensity of that
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+   %  voxel can be used by the cursor location in the transformed volume.
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+   %
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+   %  First, we traverse along Z axis of transformed volume voxel by voxel
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+   %
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+   for z = 1:new_dim(3)
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+
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+      if verbose & ~mod(z,10)
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+         fprintf('%.2f percent is done.\n', 100*z/new_dim(3));
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+      end
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+
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+      %  We need to find out the mapping from voxel in the transformed
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+      %  volume (new_XYZvox) to voxel in the original volume (old_XYZvox)
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+      %
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+      %  The following equation works, because they all equal to XYZmm:
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+      %  new_R*(new_XYZvox-1) + new_T  ==  old_R*(old_XYZvox-1) + old_T
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+      %
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+      %  We can use modified new_M1 & old_M1 to substitute new_M & old_M
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+      %      new_M1 * new_XYZvox       ==       old_M1 * old_XYZvox
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+      %
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+      %  where: M1 = M;   M1(:,4) = M(:,4) - sum(M(:,1:3),2);
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+      %  and:             M(:,4) == [T; 1] == sum(M1,2)
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+      %
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+      %  Therefore:   old_XYZvox = old_M1 \ new_M1 * new_XYZvox;
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+      %
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+      %  Since we are traverse Z axis, and   new_XYZvox   is replaced
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+      %  by   mask_Z * new_XYZvox, the above formula can be rewritten
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+      %  as:    old_XYZvox = old_M1 \ new_M1 * mask_Z * new_XYZvox;
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+      %
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+      %  i.e. we find the mapping from new_XYZvox to old_XYZvox:
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+      %  M = old_M1 \ new_M1 * mask_Z;
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+      %
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+      %  First, compute modified old_M1 & new_M1
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+      %
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+      old_M1 = old_M;   old_M1(:,4) = old_M(:,4) - sum(old_M(:,1:3),2);
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+      new_M1 = new_M;   new_M1(:,4) = new_M(:,4) - sum(new_M(:,1:3),2);
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+
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+      %  Then, apply unit increment of mask_Z(3,4) to simulate the
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+      %  cursor movement
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+      %
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+      mask_Z(3,4) = z;
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+
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+      %  Here is the mapping from new_XYZvox to old_XYZvox
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+      %
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+      M = old_M1 \ new_M1 * mask_Z;
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+
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+      switch method
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+      case 1
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+         new_img(:,:,z) = trilinear(old_img, new_dim, old_dim, M, bg);
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+      case 2
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+         new_img(:,:,z) = nearest_neighbor(old_img, new_dim, old_dim, M, bg);
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+      case 3
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+         new_img(:,:,z) = bresenham(old_img, new_dim, old_dim, M, bg);
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+      end
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+
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+   end;			% for z
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+
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+   if ndims(old_img) == 2
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+      new_M(3,:) = [];
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+      new_M(:,3) = [];
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+   end
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+
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+   return;					% affine
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+
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+
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+%--------------------------------------------------------------------
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+function img_slice = trilinear(img, dim1, dim2, M, bg)
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+
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+   img_slice = zeros(dim1(1:2));
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+   TINY = 5e-2;					% tolerance
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+
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+   %  Dimension of transformed 3D volume
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+   %
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+   xdim1 = dim1(1);
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+   ydim1 = dim1(2);
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+
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+   %  Dimension of original 3D volume
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+   %
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+   xdim2 = dim2(1);
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+   ydim2 = dim2(2);
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+   zdim2 = dim2(3);
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+
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+   %  initialize new_Y accumulation
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+   %
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+   Y2X = 0;
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+   Y2Y = 0;
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+   Y2Z = 0;
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+
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+   for y = 1:ydim1
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+
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+      %  increment of new_Y accumulation
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+      %
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+      Y2X = Y2X + M(1,2);		% new_Y to old_X
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+      Y2Y = Y2Y + M(2,2);		% new_Y to old_Y
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+      Y2Z = Y2Z + M(3,2);		% new_Y to old_Z
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+
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+      %  backproject new_Y accumulation and translation to old_XYZ
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+      %
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+      old_X = Y2X + M(1,4);
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+      old_Y = Y2Y + M(2,4);
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+      old_Z = Y2Z + M(3,4);
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+
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+      for x = 1:xdim1
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+
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+         %  accumulate the increment of new_X, and apply it
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+         %  to the backprojected old_XYZ
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+         %
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+         old_X = M(1,1) + old_X  ;
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+         old_Y = M(2,1) + old_Y  ;
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+         old_Z = M(3,1) + old_Z  ;
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+
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+         %  within boundary of original image
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+         %
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+         if (	old_X > 1-TINY & old_X < xdim2+TINY & ...
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+		old_Y > 1-TINY & old_Y < ydim2+TINY & ...
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+		old_Z > 1-TINY & old_Z < zdim2+TINY	)
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+
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+            %  Calculate distance of old_XYZ to its neighbors for
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+            %  weighted intensity average
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+            %
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+            dx = old_X - floor(old_X);
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+            dy = old_Y - floor(old_Y);
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+            dz = old_Z - floor(old_Z);
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+
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+            x000 = floor(old_X);
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+            x100 = x000 + 1;
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+
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+            if floor(old_X) < 1
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+               x000 = 1;
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+               x100 = x000;
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+            elseif floor(old_X) > xdim2-1
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+               x000 = xdim2;
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+               x100 = x000;
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+            end
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+
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+            x010 = x000;
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+            x001 = x000;
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+            x011 = x000;
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+
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+            x110 = x100;
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+            x101 = x100;
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+            x111 = x100;
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+
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+            y000 = floor(old_Y);
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+            y010 = y000 + 1;
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+
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+            if floor(old_Y) < 1
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+               y000 = 1;
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+               y100 = y000;
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+            elseif floor(old_Y) > ydim2-1
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+               y000 = ydim2;
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+               y010 = y000;
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+            end
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+
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+            y100 = y000;
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+            y001 = y000;
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+            y101 = y000;
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+
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+            y110 = y010;
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+            y011 = y010;
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+            y111 = y010;
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+
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+            z000 = floor(old_Z);
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+            z001 = z000 + 1;
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+
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+            if floor(old_Z) < 1
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+               z000 = 1;
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+               z001 = z000;
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+            elseif floor(old_Z) > zdim2-1
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+               z000 = zdim2;
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+               z001 = z000;
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+            end
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+
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+            z100 = z000;
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+            z010 = z000;
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+            z110 = z000;
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+
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+            z101 = z001;
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+            z011 = z001;
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+            z111 = z001;
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+
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+            x010 = x000;
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+            x001 = x000;
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+            x011 = x000;
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+
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+            x110 = x100;
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+            x101 = x100;
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+            x111 = x100;
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+
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+            v000 = double(img(x000, y000, z000));
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+            v010 = double(img(x010, y010, z010));
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+            v001 = double(img(x001, y001, z001));
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+            v011 = double(img(x011, y011, z011));
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+
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+            v100 = double(img(x100, y100, z100));
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+            v110 = double(img(x110, y110, z110));
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+            v101 = double(img(x101, y101, z101));
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+            v111 = double(img(x111, y111, z111));
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+
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+            img_slice(x,y) = v000*(1-dx)*(1-dy)*(1-dz) + ...
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+               v010*(1-dx)*dy*(1-dz) + ...
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+               v001*(1-dx)*(1-dy)*dz + ...
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+               v011*(1-dx)*dy*dz + ...
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+               v100*dx*(1-dy)*(1-dz) + ...
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+               v110*dx*dy*(1-dz) + ...
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+               v101*dx*(1-dy)*dz + ...
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+               v111*dx*dy*dz;
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+
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+         else
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+            img_slice(x,y) = bg;
397 
+
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+         end	% if boundary
399 
+
400 
+      end	% for x
401 
+   end		% for y
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+
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+   return;					% trilinear
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+
405 
+
406 
+%--------------------------------------------------------------------
407 
+function img_slice = nearest_neighbor(img, dim1, dim2, M, bg)
408 
+
409 
+   img_slice = zeros(dim1(1:2));
410 
+
411 
+   %  Dimension of transformed 3D volume
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+   %
413 
+   xdim1 = dim1(1);
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+   ydim1 = dim1(2);
415 
+
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+   %  Dimension of original 3D volume
417 
+   %
418 
+   xdim2 = dim2(1);
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+   ydim2 = dim2(2);
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+   zdim2 = dim2(3);
421 
+
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+   %  initialize new_Y accumulation
423 
+   %
424 
+   Y2X = 0;
425 
+   Y2Y = 0;
426 
+   Y2Z = 0;
427 
+
428 
+   for y = 1:ydim1
429 
+
430 
+      %  increment of new_Y accumulation
431 
+      %
432 
+      Y2X = Y2X + M(1,2);		% new_Y to old_X
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+      Y2Y = Y2Y + M(2,2);		% new_Y to old_Y
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+      Y2Z = Y2Z + M(3,2);		% new_Y to old_Z
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+
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+      %  backproject new_Y accumulation and translation to old_XYZ
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+      %
438 
+      old_X = Y2X + M(1,4);
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+      old_Y = Y2Y + M(2,4);
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+      old_Z = Y2Z + M(3,4);
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+
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+      for x = 1:xdim1
443 
+
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+         %  accumulate the increment of new_X and apply it
445 
+         %  to the backprojected old_XYZ
446 
+         %
447 
+         old_X = M(1,1) + old_X  ;
448 
+         old_Y = M(2,1) + old_Y  ;
449 
+         old_Z = M(3,1) + old_Z  ;
450 
+
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+         xi = round(old_X);
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+         yi = round(old_Y);
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+         zi = round(old_Z);
454 
+
455 
+         %  within boundary of original image
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+         %
457 
+         if (	xi >= 1 & xi <= xdim2 & ...
458 
+		yi >= 1 & yi <= ydim2 & ...
459 
+		zi >= 1 & zi <= zdim2	)
460 
+
461 
+            img_slice(x,y) = img(xi,yi,zi);
462 
+
463 
+         else
464 
+            img_slice(x,y) = bg;
465 
+
466 
+         end	% if boundary
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+
468 
+      end	% for x
469 
+   end		% for y
470 
+
471 
+   return;					% nearest_neighbor
472 
+
473 
+
474 
+%--------------------------------------------------------------------
475 
+function img_slice = bresenham(img, dim1, dim2, M, bg)
476 
+
477 
+   img_slice = zeros(dim1(1:2));
478 
+
479 
+   %  Dimension of transformed 3D volume
480 
+   %
481 
+   xdim1 = dim1(1);
482 
+   ydim1 = dim1(2);
483 
+
484 
+   %  Dimension of original 3D volume
485 
+   %
486 
+   xdim2 = dim2(1);
487 
+   ydim2 = dim2(2);
488 
+   zdim2 = dim2(3);
489 
+
490 
+   for y = 1:ydim1
491 
+
492 
+      start_old_XYZ = round(M*[0     y 0 1]');
493 
+      end_old_XYZ   = round(M*[xdim1 y 0 1]');
494 
+
495 
+      [X Y Z] = bresenham_line3d(start_old_XYZ, end_old_XYZ);
496 
+
497 
+      %  line error correction
498 
+      %
499 
+%      del = end_old_XYZ - start_old_XYZ;
500 
+ %     del_dom = max(del);
501 
+  %    idx_dom = find(del==del_dom);
502 
+   %   idx_dom = idx_dom(1);
503 
+    %  idx_other = [1 2 3];
504 
+     % idx_other(idx_dom) = [];
505 
+      %del_x1 = del(idx_other(1));
506 
+%      del_x2 = del(idx_other(2));
507 
+ %     line_slope = sqrt((del_x1/del_dom)^2 + (del_x2/del_dom)^2 + 1);
508 
+  %    line_error = line_slope - 1;
509 
+% line error correction removed because it is too slow
510 
+
511 
+      for x = 1:xdim1
512 
+
513 
+         %  rescale ratio
514 
+         %
515 
+         i = round(x * length(X) / xdim1);
516 
+
517 
+         if i < 1
518 
+            i = 1;
519 
+         elseif i > length(X)
520 
+            i = length(X);
521 
+         end
522 
+
523 
+         xi = X(i);
524 
+         yi = Y(i);
525 
+         zi = Z(i);
526 
+
527 
+         %  within boundary of the old XYZ space
528 
+         %
529 
+         if (	xi >= 1 & xi <= xdim2 & ...
530 
+		yi >= 1 & yi <= ydim2 & ...
531 
+		zi >= 1 & zi <= zdim2	)
532 
+
533 
+            img_slice(x,y) = img(xi,yi,zi);
534 
+
535 
+%            if line_error > 1
536 
+ %              x = x + 1;
537 
+
538 
+%               if x <= xdim1
539 
+ %                 img_slice(x,y) = img(xi,yi,zi);
540 
+  %                line_error = line_slope - 1;
541 
+   %            end
542 
+    %        end		% if line_error
543 
+% line error correction removed because it is too slow
544 
+
545 
+         else
546 
+            img_slice(x,y) = bg;
547 
+
548 
+         end	% if boundary
549 
+
550 
+      end	% for x
551 
+   end		% for y
552 
+
553 
+   return;					% bresenham
554 
+
NIFTI_20090325/bipolar.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,94 @@
1 
+%BIPOLAR returns an M-by-3 matrix containing a blue-red colormap, in
2 
+%	in which red stands for positive, blue stands for negative,
3 
+%	and white stands for 0.
4 
+%
5 
+%  Usage: cmap = bipolar(M, lo, hi, contrast);  or  cmap = bipolar;
6 
+%
7 
+%  cmap:  output M-by-3 matrix for BIPOLAR colormap.
8 
+%  M:	  number of shades in the colormap. By default, it is the
9 
+%	  same length as the current colormap.
10 
+%  lo:	  the lowest value to represent.
11 
+%  hi:	  the highest value to represent.
12 
+%
13 
+%  Inspired from the LORETA PASCAL program:
14 
+%	http://www.unizh.ch/keyinst/NewLORETA
15 
+%
16 
+%  jimmy@rotman-baycrest.on.ca
17 
+%
18 
+%----------------------------------------------------------------
19 
+function cmap = bipolar(M, lo, hi, contrast)
20 
+
21 
+   if ~exist('contrast','var')
22 
+      contrast = 128;
23 
+   end
24 
+
25 
+   if ~exist('lo','var')
26 
+      lo = -1;
27 
+   end
28 
+
29 
+   if ~exist('hi','var')
30 
+      hi = 1;
31 
+   end
32 
+
33 
+   if ~exist('M','var')
34 
+      cmap = colormap;
35 
+      M = size(cmap,1);
36 
+   end
37 
+
38 
+   steepness = 10 ^ (1 - (contrast-1)/127);
39 
+   pos_infs = 1e-99;
40 
+   neg_infs = -1e-99;
41 
+
42 
+   doubleredc = [];
43 
+   doublebluec = [];
44 
+
45 
+   if lo >= 0		% all positive
46 
+
47 
+      if lo == 0
48 
+         lo = pos_infs;
49 
+      end
50 
+
51 
+      for i=linspace(hi/M, hi, M)
52 
+         t = exp(log(i/hi)*steepness);
53 
+         doubleredc = [doubleredc; [(1-t)+t,(1-t)+0,(1-t)+0]];
54 
+      end
55 
+
56 
+      cmap = doubleredc;
57 
+
58 
+   elseif hi <= 0	% all negative
59 
+
60 
+      if hi == 0
61 
+         hi = neg_infs;
62 
+      end
63 
+
64 
+      for i=linspace(abs(lo)/M, abs(lo), M)
65 
+         t = exp(log(i/abs(lo))*steepness);
66 
+         doublebluec = [doublebluec; [(1-t)+0,(1-t)+0,(1-t)+t]];
67 
+      end
68 
+
69 
+      cmap = flipud(doublebluec);
70 
+
71 
+   else
72 
+
73 
+      if hi > abs(lo)
74 
+         maxc = hi;
75 
+      else
76 
+         maxc = abs(lo);
77 
+      end
78 
+
79 
+      for i=linspace(maxc/M, hi, round(M*hi/(hi-lo)))
80 
+         t = exp(log(i/maxc)*steepness);
81 
+         doubleredc = [doubleredc; [(1-t)+t,(1-t)+0,(1-t)+0]];
82 
+      end
83 
+
84 
+      for i=linspace(maxc/M, abs(lo), round(M*abs(lo)/(hi-lo)))
85 
+         t = exp(log(i/maxc)*steepness);
86 
+         doublebluec = [doublebluec; [(1-t)+0,(1-t)+0,(1-t)+t]];
87 
+      end
88 
+
89 
+      cmap = [flipud(doublebluec); doubleredc];
90 
+
91 
+   end
92 
+
93 
+   return;					% bipolar
94 
+
NIFTI_20090325/bresenham_line3d.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,189 @@
1 
+%  Generate X Y Z coordinates of a 3D Bresenham's line between
2 
+%  two given points.
3 
+%
4 
+%  A very useful application of this algorithm can be found in the
5 
+%  implementation of Fischer's Bresenham interpolation method in my
6 
+%  another program that can rotate three dimensional image volume
7 
+%  with an affine matrix:
8 
+%  http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=21080
9 
+%
10 
+%  Usage: [X Y Z] = bresenham_line3d(P1, P2, [precision]);
11 
+%
12 
+%  P1	- vector for Point1, where P1 = [x1 y1 z1]
13 
+%
14 
+%  P2	- vector for Point2, where P2 = [x2 y2 z2]
15 
+%
16 
+%  precision (optional) - Although according to Bresenham's line
17 
+%	algorithm, point coordinates x1 y1 z1 and x2 y2 z2 should
18 
+%	be integer numbers, this program extends its limit to all
19 
+%	real numbers. If any of them are floating numbers, you
20 
+%	should specify how many digits of decimal that you would
21 
+%	like to preserve. Be aware that the length of output X Y
22 
+%	Z coordinates will increase in 10 times for each decimal
23 
+%	digit that you want to preserve. By default, the precision
24 
+%	is 0, which means that they will be rounded to the nearest
25 
+%	integer.
26 
+%
27 
+%  X	- a set of x coordinates on Bresenham's line
28 
+%
29 
+%  Y	- a set of y coordinates on Bresenham's line
30 
+%
31 
+%  Z	- a set of z coordinates on Bresenham's line
32 
+%
33 
+%  Therefore, all points in XYZ set (i.e. P(i) = [X(i) Y(i) Z(i)])
34 
+%  will constitute the Bresenham's line between P1 and P1.
35 
+%
36 
+%  Example:
37 
+%	P1 = [12 37 6];     P2 = [46 3 35];
38 
+%	[X Y Z] = bresenham_line3d(P1, P2);
39 
+%	figure; plot3(X,Y,Z,'s','markerface','b');
40 
+%
41 
+%  This program is ported to MATLAB from:
42 
+%
43 
+%  B.Pendleton.  line3d - 3D Bresenham's (a 3D line drawing algorithm)
44 
+%  ftp://ftp.isc.org/pub/usenet/comp.sources.unix/volume26/line3d, 1992
45 
+%
46 
+%  Which is also referenced by:
47 
+%
48 
+%  Fischer, J., A. del Rio (2004).  A Fast Method for Applying Rigid
49 
+%  Transformations to Volume Data, WSCG2004 Conference.
50 
+%  http://wscg.zcu.cz/wscg2004/Papers_2004_Short/M19.pdf
51 
+%
52 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
53 
+%
54 
+function [X,Y,Z] = bresenham_line3d(P1, P2, precision)
55 
+
56 
+   if ~exist('precision','var') | isempty(precision) | round(precision) == 0
57 
+      precision = 0;
58 
+      P1 = round(P1);
59 
+      P2 = round(P2);
60 
+   else
61 
+      precision = round(precision);
62 
+      P1 = round(P1*(10^precision));
63 
+      P2 = round(P2*(10^precision));
64 
+   end
65 
+
66 
+   d = max(abs(P2-P1)+1);
67 
+   X = zeros(1, d);
68 
+   Y = zeros(1, d);
69 
+   Z = zeros(1, d);
70 
+
71 
+   x1 = P1(1);
72 
+   y1 = P1(2);
73 
+   z1 = P1(3);
74 
+
75 
+   x2 = P2(1);
76 
+   y2 = P2(2);
77 
+   z2 = P2(3);
78 
+
79 
+   dx = x2 - x1;
80 
+   dy = y2 - y1;
81 
+   dz = z2 - z1;
82 
+
83 
+   ax = abs(dx)*2;
84 
+   ay = abs(dy)*2;
85 
+   az = abs(dz)*2;
86 
+
87 
+   sx = sign(dx);
88 
+   sy = sign(dy);
89 
+   sz = sign(dz);
90 
+
91 
+   x = x1;
92 
+   y = y1;
93 
+   z = z1;
94 
+   idx = 1;
95 
+
96 
+   if(ax>=max(ay,az))			% x dominant
97 
+      yd = ay - ax/2;
98 
+      zd = az - ax/2;
99 
+
100 
+      while(1)
101 
+         X(idx) = x;
102 
+         Y(idx) = y;
103 
+         Z(idx) = z;
104 
+         idx = idx + 1;
105 
+
106 
+         if(x == x2)		% end
107 
+            break;
108 
+         end
109 
+
110 
+         if(yd >= 0)		% move along y
111 
+            y = y + sy;
112 
+            yd = yd - ax;
113 
+         end
114 
+
115 
+         if(zd >= 0)		% move along z
116 
+            z = z + sz;
117 
+            zd = zd - ax;
118 
+         end
119 
+
120 
+         x  = x  + sx;		% move along x
121 
+         yd = yd + ay;
122 
+         zd = zd + az;
123 
+      end
124 
+   elseif(ay>=max(ax,az))		% y dominant
125 
+      xd = ax - ay/2;
126 
+      zd = az - ay/2;
127 
+
128 
+      while(1)
129 
+         X(idx) = x;
130 
+         Y(idx) = y;
131 
+         Z(idx) = z;
132 
+         idx = idx + 1;
133 
+
134 
+         if(y == y2)		% end
135 
+            break;
136 
+         end
137 
+
138 
+         if(xd >= 0)		% move along x
139 
+            x = x + sx;
140 
+            xd = xd - ay;
141 
+         end
142 
+
143 
+         if(zd >= 0)		% move along z
144 
+            z = z + sz;
145 
+            zd = zd - ay;
146 
+         end
147 
+
148 
+         y  = y  + sy;		% move along y
149 
+         xd = xd + ax;
150 
+         zd = zd + az;
151 
+      end
152 
+   elseif(az>=max(ax,ay))		% z dominant
153 
+      xd = ax - az/2;
154 
+      yd = ay - az/2;
155 
+
156 
+      while(1)
157 
+         X(idx) = x;
158 
+         Y(idx) = y;
159 
+         Z(idx) = z;
160 
+         idx = idx + 1;
161 
+
162 
+         if(z == z2)		% end
163 
+            break;
164 
+         end
165 
+
166 
+         if(xd >= 0)		% move along x
167 
+            x = x + sx;
168 
+            xd = xd - az;
169 
+         end
170 
+
171 
+         if(yd >= 0)		% move along y
172 
+            y = y + sy;
173 
+            yd = yd - az;
174 
+         end
175 
+
176 
+         z  = z  + sz;		% move along z
177 
+         xd = xd + ax;
178 
+         yd = yd + ay;
179 
+      end
180 
+   end
181 
+
182 
+   if precision ~= 0
183 
+      X = X/(10^precision);
184 
+      Y = Y/(10^precision);
185 
+      Z = Z/(10^precision);
186 
+   end
187 
+
188 
+   return;					% bresenham_line3d
189 
+
NIFTI_20090325/collapse_nii_scan.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,202 @@
1 
+%  Collapse multiple single-scan NIFTI files into a multiple-scan NIFTI file
2 
+%
3 
+%  Usage: collapse_nii_scan(scan_file_pattern, [collapsed_filename], [scan_file_folder])
4 
+%
5 
+%  Here, scan_file_pattern should look like: 'myscan_0*.img'
6 
+%  If collapsed_filename is omit, 'multi_scan.nii' will be used
7 
+%  If scan_file_folder is omit, current file folder will be used
8 
+%
9 
+%  The order of volumes in the collapsed file will be the order of
10 
+%  corresponding filenames for those selected scan files.
11 
+%
12 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
13 
+%
14 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
15 
+%
16 
+function collapse_nii_scan(scan_pattern, fileprefix, scan_path)
17 
+
18 
+   if ~exist('fileprefix','var'), fileprefix = 'multi_scan.nii'; end
19 
+   if ~exist('scan_path','var'), scan_path = pwd; end
20 
+
21 
+   filetype = 1;
22 
+
23 
+   %  Note: fileprefix is actually the filename you want to save
24 
+   %
25 
+   if findstr('.nii',fileprefix)
26 
+      filetype = 2;
27 
+      fileprefix = strrep(fileprefix,'.nii','');
28 
+   end
29 
+
30 
+   if findstr('.hdr',fileprefix)
31 
+      fileprefix = strrep(fileprefix,'.hdr','');
32 
+   end
33 
+
34 
+   if findstr('.img',fileprefix)
35 
+      fileprefix = strrep(fileprefix,'.img','');
36 
+   end
37 
+
38 
+   pnfn = fullfile(scan_path, scan_pattern);
39 
+
40 
+   file_lst = dir(pnfn);
41 
+   flist = {file_lst.name};
42 
+   flist = flist(:);
43 
+
44 
+   nii = load_nii(flist{1});
45 
+   nii.hdr.dime.dim(5) = length(flist);
46 
+   hdr = nii.hdr;
47 
+
48 
+   if isfield(nii,'ext') & ~isempty(nii.ext)
49 
+      ext = nii.ext;
50 
+      [ext, esize_total] = verify_nii_ext(ext);
51 
+   else
52 
+      ext = [];
53 
+   end
54 
+
55 
+   switch double(hdr.dime.datatype),
56 
+   case   1,
57 
+      hdr.dime.bitpix = int16(1 ); precision = 'ubit1';
58 
+   case   2,
59 
+      hdr.dime.bitpix = int16(8 ); precision = 'uint8';
60 
+   case   4,
61 
+      hdr.dime.bitpix = int16(16); precision = 'int16';
62 
+   case   8,
63 
+      hdr.dime.bitpix = int16(32); precision = 'int32';
64 
+   case  16,
65 
+      hdr.dime.bitpix = int16(32); precision = 'float32';
66 
+   case  32,
67 
+      hdr.dime.bitpix = int16(64); precision = 'float32';
68 
+   case  64,
69 
+      hdr.dime.bitpix = int16(64); precision = 'float64';
70 
+   case 128,
71 
+      hdr.dime.bitpix = int16(24); precision = 'uint8';
72 
+   case 256
73 
+      hdr.dime.bitpix = int16(8 ); precision = 'int8';
74 
+   case 512
75 
+      hdr.dime.bitpix = int16(16); precision = 'uint16';
76 
+   case 768
77 
+      hdr.dime.bitpix = int16(32); precision = 'uint32';
78 
+   case 1024
79 
+      hdr.dime.bitpix = int16(64); precision = 'int64';
80 
+   case 1280
81 
+      hdr.dime.bitpix = int16(64); precision = 'uint64';
82 
+   case 1792,
83 
+      hdr.dime.bitpix = int16(128); precision = 'float64';
84 
+   otherwise
85 
+      error('This datatype is not supported');
86 
+   end
87 
+
88 
+   if filetype == 2
89 
+      fid = fopen(sprintf('%s.nii',fileprefix),'w');
90 
+
91 
+      if fid < 0,
92 
+         msg = sprintf('Cannot open file %s.nii.',fileprefix);
93 
+         error(msg);
94 
+      end
95 
+
96 
+      hdr.dime.vox_offset = 352;
97 
+
98 
+      if ~isempty(ext)
99 
+         hdr.dime.vox_offset = hdr.dime.vox_offset + esize_total;
100 
+      end
101 
+
102 
+      hdr.hist.magic = 'n+1';
103 
+      save_nii_hdr(hdr, fid);
104 
+
105 
+      if ~isempty(ext)
106 
+         save_nii_ext(ext, fid);
107 
+      end
108 
+   else
109 
+      fid = fopen(sprintf('%s.hdr',fileprefix),'w');
110 
+
111 
+      if fid < 0,
112 
+         msg = sprintf('Cannot open file %s.hdr.',fileprefix);
113 
+         error(msg);
114 
+      end
115 
+
116 
+      hdr.dime.vox_offset = 0;
117 
+      hdr.hist.magic = 'ni1';
118 
+      save_nii_hdr(hdr, fid);
119 
+
120 
+      if ~isempty(ext)
121 
+         save_nii_ext(ext, fid);
122 
+      end
123 
+
124 
+      fclose(fid);
125 
+      fid = fopen(sprintf('%s.img',fileprefix),'w');
126 
+   end
127 
+
128 
+   if filetype == 2 & isempty(ext)
129 
+      skip_bytes = double(hdr.dime.vox_offset) - 348;
130 
+   else
131 
+      skip_bytes = 0;
132 
+   end
133 
+
134 
+   glmax = -inf;
135 
+   glmin = inf;
136 
+
137 
+   for i = 1:length(flist)
138 
+      nii = load_nii(flist{i});
139 
+
140 
+      if double(hdr.dime.datatype) == 128
141 
+
142 
+         %  RGB planes are expected to be in the 4th dimension of nii.img
143 
+         %
144 
+         if(size(nii.img,4)~=3)
145 
+            error(['The NII structure does not appear to have 3 RGB color planes in the 4th dimension']);
146 
+         end
147 
+
148 
+         if old_RGB
149 
+            nii.img = permute(nii.img, [1 2 4 3 5 6 7 8]);
150 
+         else
151 
+            nii.img = permute(nii.img, [4 1 2 3 5 6 7 8]);
152 
+         end
153 
+      end
154 
+
155 
+      %  For complex float32 or complex float64, voxel values
156 
+      %  include [real, imag]
157 
+      %
158 
+      if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
159 
+         real_img = real(nii.img(:))';
160 
+         nii.img = imag(nii.img(:))';
161 
+         nii.img = [real_img; nii.img];
162 
+      end
163 
+
164 
+      if nii.hdr.dime.glmax > glmax
165 
+         glmax = nii.hdr.dime.glmax;
166 
+      end
167 
+
168 
+      if nii.hdr.dime.glmin < glmin
169 
+         glmin = nii.hdr.dime.glmin;
170 
+      end
171 
+
172 
+      fwrite(fid, nii.img, precision);
173 
+   end
174 
+
175 
+   hdr.dime.glmax = round(glmax);
176 
+   hdr.dime.glmin = round(glmin);
177 
+
178 
+   if filetype == 2
179 
+      fseek(fid, 140, 'bof');
180 
+      fwrite(fid, hdr.dime.glmax, 'int32');
181 
+      fwrite(fid, hdr.dime.glmin, 'int32');
182 
+   else
183 
+      fid2 = fopen(sprintf('%s.hdr',fileprefix),'w');
184 
+
185 
+      if fid2 < 0,
186 
+         msg = sprintf('Cannot open file %s.hdr.',fileprefix);
187 
+         error(msg);
188 
+      end
189 
+
190 
+      save_nii_hdr(hdr, fid2);
191 
+
192 
+      if ~isempty(ext)
193 
+         save_nii_ext(ext, fid2);
194 
+      end
195 
+
196 
+      fclose(fid2);
197 
+   end
198 
+
199 
+   fclose(fid);
200 
+
201 
+   return;					% collapse_nii_scan
202 
+
NIFTI_20090325/examples.txt
Zeige Datei @ 87b08fd
... ... 
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+
2 
+- Examples to load, make and save a nii struct:
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+
4 
+	To load Analyze data or NIFTI data to a structure:
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+
6 
+		nii = load_nii(NIFTI_file_name, [img_idx], [old_RGB24]);
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+
8 
+	img_idx is a numerical array of image indices along the temporal
9 
+	axis, which is only available in NIFTI data. After you specify
10 
+	img_idx, only those images indexed by img_idx will be loaded. If
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+	there is no img_idx or img_idx is empty, all available images
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+	will be loaded.
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+
14 
+	For RGB image, most people use RGB triple sequentially for each
15 
+	voxel, like [R1 G1 B1 R2 G2 B2 ...]. However, some program like
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+	Analyze 6.0 developed by AnalyzeDirect uses old RGB24, in a way
17 
+	like [R1 R2 ... G1 G2 ... B1 B2 ...] for each slices. In this
18 
+	case, you can set old_RGB24 flag to 1 and load data correctly:
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+
20 
+		nii = load_nii(NIFTI_file_name, [], 1);
21 
+
22 
+	To get a total number of images along the temporal axis:
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+
24 
+		num_scan = get_nii_frame(NIFTI_file_name);
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+
26 
+	You can also load the header extension if it exists:
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+
28 
+		nii.ext = load_nii_ext(NIFTI_file_name);
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+
30 
+	You can just load the Analyze or NIFTI header:
31 
+	(header contains: hk, dime, and hist)
32 
+
33 
+		hdr = load_nii_hdr(NIFTI_file_name);
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+
35 
+	You can also save the structure to a new file:
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+	(header extension will be saved if there is nii.ext structure)
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+
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+		save_nii(nii, NIFTI_file_name);
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+
40 
+	To make the structure from any 3D (or 4D) data:
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+
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+		img = rand(91,109,91); or
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+		img = rand(64,64,21,18);
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+		nii = make_nii(img [, voxel_size, origin, datatype] );
45 
+
46 
+	Use "help load_nii", "help save_nii", "help make_nii" etc.
47 
+	to get more detail information.
48 
+
49 
+
50 
+- Examples to plot a nii struct:
51 
+  (More detail descriptions are available on top of "view_nii.m")
52 
+
53 
+	Simple way to plot a nii struct:
54 
+
55 
+		view_nii(nii);
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+
57 
+	The default colormap will use the Gray if all data values are
58 
+	non-negative; otherwise, the default colormap will use BiPolar.
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+	You can choose other colormap, including customized colormap
60 
+	from panel.
61 
+
62 
+	To imbed the plot into your existing figure:
63 
+
64 
+		h = gcf;
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+		opt.command = 'init';
66 
+		opt.setarea = [0.3 0.1 0.6 0.8];
67 
+		view_nii(h, nii, opt);
68 
+
69 
+	To add a colorbar:
70 
+
71 
+		opt.usecolorbar = 1;
72 
+		view_nii(gcf, opt);
73 
+
74 
+		Here, opt.command is implicitly set to 'update'.
75 
+
76 
+	To display in real aspect ratio:
77 
+
78 
+		opt.usestretch = 0;
79 
+		view_nii(gcf, opt);
80 
+
81 
+	If you want the data value to be directly used as the index
82 
+	of colormap, instead of scale to the whole colormap:
83 
+
84 
+		opt.useimagesc = 0;
85 
+		view_nii(gcf, opt);
86 
+
87 
+	If you modified the data value without changing the dimension,
88 
+	voxel_size, and origin, you can update the display by:
89 
+
90 
+		opt.command = 'updateimg';
91 
+		view_nii(gcf, nii.img, opt);
92 
+
93 
+	If the data is completely different, display can be updated by:
94 
+
95 
+		opt.command = 'updatenii';
96 
+		view_nii(gcf, nii, opt);
97 
+
98 
+
99 
+- Contrast and Brightness are available under Gray and Bipolar colormap:
100 
+
101 
+
102 
+	Increase contrast in Gray colormap will make high end values
103 
+	more distinguishable by sacrificing the low end values; The
104 
+	minimum contrast (default) will display the whole range.
105 
+
106 
+	Increase or decrease contrast in BiPolar colormap will shift
107 
+	the distinguishable position for both positive and negative
108 
+	values.
109 
+
110 
+	Increase or decrease brightness in Gray colormap will shift
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+	the distinguishable position.
112 
+
113 
+	Increase or decrease brightness in BiPolar colormap will make
114 
+	both positive and negative values more distinguishable.
115 
+
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+
117 
+- Required files:
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+
119 
+	All files in this package.
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+
NIFTI_20090325/expand_nii_scan.m
Zeige Datei @ 87b08fd
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1 
+%  Expand a multiple-scan NIFTI file into multiple single-scan NIFTI files
2 
+%
3 
+%  Usage: expand_nii_scan(multi_scan_filename, [img_idx], [path_to_save])
4 
+%
5 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
6 
+%
7 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
8 
+%
9 
+function expand_nii_scan(filename, img_idx, newpath)
10 
+
11 
+   if ~exist('newpath','var'), newpath = pwd; end
12 
+   if ~exist('img_idx','var'), img_idx = 1:get_nii_frame(filename); end
13 
+
14 
+   for i=img_idx
15 
+      nii_i = load_nii(filename, i);
16 
+
17 
+      fn = [nii_i.fileprefix '_' sprintf('%04d',i)];
18 
+      pnfn = fullfile(newpath, fn);
19 
+
20 
+      save_nii(nii_i, pnfn);
21 
+   end
22 
+
23 
+   return;					% expand_nii_scan
24 
+
NIFTI_20090325/extra_nii_hdr.m
Zeige Datei @ 87b08fd
... ... 
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1 
+%  Decode extra NIFTI header information into hdr.extra
2 
+%
3 
+%  Usage: hdr = extra_nii_hdr(hdr)
4 
+%
5 
+%  hdr can be obtained from load_nii_hdr
6 
+%
7 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
8 
+%
9 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
10 
+%
11 
+function hdr = extra_nii_hdr(hdr)
12 
+
13 
+   switch hdr.dime.datatype
14 
+   case 1
15 
+      extra.NIFTI_DATATYPES = 'DT_BINARY';
16 
+   case 2
17 
+      extra.NIFTI_DATATYPES = 'DT_UINT8';
18 
+   case 4
19 
+      extra.NIFTI_DATATYPES = 'DT_INT16';
20 
+   case 8
21 
+      extra.NIFTI_DATATYPES = 'DT_INT32';
22 
+   case 16
23 
+      extra.NIFTI_DATATYPES = 'DT_FLOAT32';
24 
+   case 32
25 
+      extra.NIFTI_DATATYPES = 'DT_COMPLEX64';
26 
+   case 64
27 
+      extra.NIFTI_DATATYPES = 'DT_FLOAT64';
28 
+   case 128
29 
+      extra.NIFTI_DATATYPES = 'DT_RGB24';
30 
+   case 256
31 
+      extra.NIFTI_DATATYPES = 'DT_INT8';
32 
+   case 512
33 
+      extra.NIFTI_DATATYPES = 'DT_UINT16';
34 
+   case 768
35 
+      extra.NIFTI_DATATYPES = 'DT_UINT32';
36 
+   case 1024
37 
+      extra.NIFTI_DATATYPES = 'DT_INT64';
38 
+   case 1280
39 
+      extra.NIFTI_DATATYPES = 'DT_UINT64';
40 
+   case 1536
41 
+      extra.NIFTI_DATATYPES = 'DT_FLOAT128';
42 
+   case 1792
43 
+      extra.NIFTI_DATATYPES = 'DT_COMPLEX128';
44 
+   case 2048
45 
+      extra.NIFTI_DATATYPES = 'DT_COMPLEX256';
46 
+   otherwise
47 
+      extra.NIFTI_DATATYPES = 'DT_UNKNOWN';
48 
+   end
49 
+
50 
+   switch hdr.dime.intent_code
51 
+   case 2
52 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CORREL';
53 
+   case 3
54 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_TTEST';
55 
+   case 4
56 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_FTEST';
57 
+   case 5
58 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_ZSCORE';
59 
+   case 6
60 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CHISQ';
61 
+   case 7
62 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_BETA';
63 
+   case 8
64 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_BINOM';
65 
+   case 9
66 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_GAMMA';
67 
+   case 10
68 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_POISSON';
69 
+   case 11
70 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_NORMAL';
71 
+   case 12
72 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_FTEST_NONC';
73 
+   case 13
74 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CHISQ_NONC';
75 
+   case 14
76 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LOGISTIC';
77 
+   case 15
78 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LAPLACE';
79 
+   case 16
80 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_UNIFORM';
81 
+   case 17
82 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_TTEST_NONC';
83 
+   case 18
84 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_WEIBULL';
85 
+   case 19
86 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CHI';
87 
+   case 20
88 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_INVGAUSS';
89 
+   case 21
90 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_EXTVAL';
91 
+   case 22
92 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_PVAL';
93 
+   case 23
94 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LOGPVAL';
95 
+   case 24
96 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LOG10PVAL';
97 
+   case 1001
98 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_ESTIMATE';
99 
+   case 1002
100 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LABEL';
101 
+   case 1003
102 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_NEURONAME';
103 
+   case 1004
104 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_GENMATRIX';
105 
+   case 1005
106 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_SYMMATRIX';
107 
+   case 1006
108 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_DISPVECT';
109 
+   case 1007
110 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_VECTOR';
111 
+   case 1008
112 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_POINTSET';
113 
+   case 1009
114 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_TRIANGLE';
115 
+   case 1010
116 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_QUATERNION';
117 
+   case 1011
118 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_DIMLESS';
119 
+   otherwise
120 
+      extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_NONE';
121 
+   end
122 
+
123 
+   extra.NIFTI_INTENT_NAMES = hdr.hist.intent_name;
124 
+
125 
+   if hdr.hist.sform_code > 0
126 
+      switch hdr.hist.sform_code
127 
+      case 1
128 
+         extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_SCANNER_ANAT';
129 
+      case 2
130 
+         extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_ALIGNED_ANAT';
131 
+      case 3
132 
+         extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_TALAIRACH';
133 
+      case 4
134 
+         extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_MNI_152';
135 
+      otherwise
136 
+         extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
137 
+      end
138 
+
139 
+      extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
140 
+   elseif hdr.hist.qform_code > 0
141 
+      extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
142 
+
143 
+      switch hdr.hist.qform_code
144 
+      case 1
145 
+         extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_SCANNER_ANAT';
146 
+      case 2
147 
+         extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_ALIGNED_ANAT';
148 
+      case 3
149 
+         extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_TALAIRACH';
150 
+      case 4
151 
+         extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_MNI_152';
152 
+      otherwise
153 
+         extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
154 
+      end
155 
+   else
156 
+      extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
157 
+      extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
158 
+   end
159 
+
160 
+   switch bitand(hdr.dime.xyzt_units, 7)	% mask with 0x07
161 
+   case 1
162 
+      extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_METER';
163 
+   case 2
164 
+      extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_MM';	% millimeter
165 
+   case 3
166 
+      extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_MICRO';
167 
+   otherwise
168 
+      extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_UNKNOWN';
169 
+   end
170 
+
171 
+   switch bitand(hdr.dime.xyzt_units, 56)	% mask with 0x38
172 
+   case 8
173 
+      extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_SEC';
174 
+   case 16
175 
+      extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_MSEC';
176 
+   case 24
177 
+      extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_USEC';	% microsecond
178 
+   otherwise
179 
+      extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_UNKNOWN';
180 
+   end
181 
+
182 
+   switch hdr.dime.xyzt_units
183 
+   case 32
184 
+      extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_HZ';
185 
+   case 40
186 
+      extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_PPM';	% part per million
187 
+   case 48
188 
+      extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_RADS';	% radians per second
189 
+   otherwise
190 
+      extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_UNKNOWN';
191 
+   end
192 
+
193 
+   %  MRI-specific spatial and temporal information
194 
+   %
195 
+   dim_info = hdr.hk.dim_info;
196 
+   extra.NIFTI_FREQ_DIM = bitand(dim_info, 3);
197 
+   extra.NIFTI_PHASE_DIM = bitand(bitshift(dim_info, -2), 3);
198 
+   extra.NIFTI_SLICE_DIM = bitand(bitshift(dim_info, -4), 3);
199 
+
200 
+   %  Check slice code
201 
+   %
202 
+   switch hdr.dime.slice_code
203 
+   case 1
204 
+      extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_SEQ_INC';	% sequential increasing
205 
+   case 2
206 
+      extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_SEQ_DEC';	% sequential decreasing
207 
+   case 3
208 
+      extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_INC';	% alternating increasing
209 
+   case 4
210 
+      extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_DEC';	% alternating decreasing
211 
+   case 5
212 
+      extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_INC2';	% ALT_INC # 2
213 
+   case 6
214 
+      extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_DEC2';	% ALT_DEC # 2
215 
+   otherwise
216 
+      extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_UNKNOWN';
217 
+   end
218 
+
219 
+   %  Check NIFTI version
220 
+   %
221 
+   if     ~isempty(hdr.hist.magic) & strcmp(hdr.hist.magic(1),'n') & ...
222 
+	( strcmp(hdr.hist.magic(2),'i') | strcmp(hdr.hist.magic(2),'+') ) & ...
223 
+	  str2num(hdr.hist.magic(3)) >= 1 & str2num(hdr.hist.magic(3)) <= 9
224 
+
225 
+      extra.NIFTI_VERSION = str2num(hdr.hist.magic(3));
226 
+   else
227 
+      extra.NIFTI_VERSION = 0;
228 
+   end
229 
+
230 
+   %  Check if data stored in the same file (*.nii) or separate
231 
+   %  files (*.hdr/*.img)
232 
+   %
233 
+   if isempty(hdr.hist.magic)
234 
+      extra.NIFTI_ONEFILE = 0;
235 
+   else
236 
+      extra.NIFTI_ONEFILE = strcmp(hdr.hist.magic(2), '+');
237 
+   end
238 
+
239 
+   %  Swap has been taken care of by checking whether sizeof_hdr is
240 
+   %  348 (machine is 'ieee-le' or 'ieee-be' etc)
241 
+   %
242 
+   % extra.NIFTI_NEEDS_SWAP = (hdr.dime.dim(1) < 0 | hdr.dime.dim(1) > 7);
243 
+
244 
+   %  Check NIFTI header struct contains a 5th (vector) dimension
245 
+   %
246 
+   if hdr.dime.dim(1) > 4 & hdr.dime.dim(6) > 1
247 
+      extra.NIFTI_5TH_DIM = hdr.dime.dim(6);
248 
+   else
249 
+      extra.NIFTI_5TH_DIM = 0;
250 
+   end
251 
+
252 
+   hdr.extra = extra;
253 
+
254 
+   return;					% extra_nii_hdr
255 
+
NIFTI_20090325/flip_lr.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,81 @@
1 
+%  When you load any ANALYZE or NIfTI file with 'load_nii.m', and view
2 
+%  it with 'view_nii.m', you may find that the image is L-R flipped.
3 
+%  This is because of the confusion of radiological and neurological
4 
+%  convention in the medical image before NIfTI format is adopted.
5 
+%
6 
+%  Sometime, people even want to convert RAS (standard orientation) back
7 
+%  to LAS orientation to satisfy the legend programs or processes. This
8 
+%  program is only written for those purpose. So PLEASE BE VERY CAUTIOUS
9 
+%  WHEN USING THIS 'FLIP_LR.M' PROGRAM.
10 
+%
11 
+%  With 'flip_lr.m', you can convert any ANALYZE or NIfTI (no matter
12 
+%  3D or 4D) file to a flipped NIfTI file. This is implemented simply
13 
+%  by flipping the affine matrix in the NIfTI header. Since the L-R
14 
+%  orientation is determined there, so the image will be flipped.
15 
+%
16 
+%  Usage: flip_lr(original_fn, flipped_fn, [old_RGB],[tolerance],[preferredForm])
17 
+%
18 
+%  original_fn  -  filename of the original ANALYZE or NIfTI (3D or 4D) file
19 
+%
20 
+%  flipped_fn  -  filename of the L-R flipped NIfTI file
21 
+%
22 
+%  old_RGB (optional)  -  a scale number to tell difference of new RGB24
23 
+%	from old RGB24. New RGB24 uses RGB triple sequentially for each
24 
+%	voxel, like [R1 G1 B1 R2 G2 B2 ...]. Analyze 6.0 from AnalyzeDirect
25 
+%	uses old RGB24, in a way like [R1 R2 ... G1 G2 ... B1 B2 ...] for
26 
+%	each slices. If the image that you view is garbled, try to set
27 
+%	old_RGB variable to 1 and try again, because it could be in
28 
+%	old RGB24. It will be set to 0, if it is default or empty.
29 
+%
30 
+%  tolerance (optional) - distortion allowed for non-orthogonal rotation
31 
+%	or shearing in NIfTI affine matrix. It will be set to 0.1 (10%),
32 
+%	if it is default or empty.
33 
+%
34 
+%  preferredForm (optional)  -  selects which transformation from voxels
35 
+%	to RAS coordinates; values are s,q,S,Q.  Lower case s,q indicate
36 
+%	"prefer sform or qform, but use others if preferred not present".
37 
+%	Upper case indicate the program is forced to use the specificied
38 
+%	tranform or fail loading.  'preferredForm' will be 's', if it is
39 
+%	default or empty.	- Jeff Gunter
40 
+%
41 
+%  Example: flip_lr('avg152T1_LR_nifti.nii', 'flipped_lr.nii');
42 
+%           flip_lr('avg152T1_RL_nifti.nii', 'flipped_rl.nii');
43 
+%
44 
+%  You will find that 'avg152T1_LR_nifti.nii' and 'avg152T1_RL_nifti.nii'
45 
+%  are the same, and 'flipped_lr.nii' and 'flipped_rl.nii' are also the
46 
+%  the same, but they are L-R flipped from 'avg152T1_*'.
47 
+%
48 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
49 
+%
50 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
51 
+%
52 
+function flip_lr(original_fn, flipped_fn, old_RGB, tolerance, preferredForm)
53 
+
54 
+   if ~exist('original_fn','var') | ~exist('flipped_fn','var')
55 
+      error('Usage: flip_lr(original_fn, flipped_fn, [old_RGB],[tolerance])');
56 
+   end
57 
+
58 
+   if ~exist('old_RGB','var') | isempty(old_RGB)
59 
+      old_RGB = 0;
60 
+   end
61 
+
62 
+   if ~exist('tolerance','var') | isempty(tolerance)
63 
+      tolerance = 0.1;
64 
+   end
65 
+
66 
+   if ~exist('preferredForm','var') | isempty(preferredForm)
67 
+      preferredForm= 's';				% Jeff
68 
+   end
69 
+
70 
+   nii = load_nii(original_fn, [], [], [], [], old_RGB, tolerance, preferredForm);
71 
+   M = diag(nii.hdr.dime.pixdim(2:5));
72 
+   M(1:3,4) = -M(1:3,1:3)*(nii.hdr.hist.originator(1:3)-1)';
73 
+   M(1,:) = -1*M(1,:);
74 
+   nii.hdr.hist.sform_code = 1;
75 
+   nii.hdr.hist.srow_x = M(1,:);
76 
+   nii.hdr.hist.srow_y = M(2,:);
77 
+   nii.hdr.hist.srow_z = M(3,:);
78 
+   save_nii(nii, flipped_fn);
79 
+
80 
+   return;					% flip_lr
81 
+
NIFTI_20090325/get_nii_frame.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,108 @@
1 
+%  Return time frame of a NIFTI dataset. Support both *.nii and
2 
+%  *.hdr/*.img file extension. If file extension is not provided,
3 
+%  *.hdr/*.img will be used as default.
4 
+%
5 
+%  It is a lightweighted "load_nii_hdr", and is equivalent to
6 
+%  hdr.dime.dim(5)
7 
+%
8 
+%  Usage: [ total_scan ] = get_nii_frame(filename)
9 
+%
10 
+%  filename - NIFTI file name.
11 
+%
12 
+%  Returned values:
13 
+%
14 
+%  total_scan - total number of image scans for the time frame
15 
+%
16 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
17 
+%
18 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
19 
+%
20 
+function [ total_scan ] = get_nii_frame(fileprefix)
21 
+
22 
+   if ~exist('fileprefix','var'),
23 
+      error('Usage: [ hdr, fileprefix, machine ] = get_nii_frame(filename)');
24 
+   end
25 
+
26 
+   if ~exist('machine','var'), machine = 'ieee-le'; end
27 
+
28 
+   new_ext = 0;
29 
+
30 
+   if findstr('.nii',fileprefix)
31 
+      new_ext = 1;
32 
+      fileprefix = strrep(fileprefix,'.nii','');
33 
+   end
34 
+
35 
+   if findstr('.hdr',fileprefix)
36 
+      fileprefix = strrep(fileprefix,'.hdr','');
37 
+   end
38 
+
39 
+   if findstr('.img',fileprefix)
40 
+      fileprefix = strrep(fileprefix,'.img','');
41 
+   end
42 
+
43 
+   if new_ext
44 
+      fn = sprintf('%s.nii',fileprefix);
45 
+
46 
+      if ~exist(fn)
47 
+         msg = sprintf('Cannot find file "%s.nii".', fileprefix);
48 
+         error(msg);
49 
+      end
50 
+   else
51 
+      fn = sprintf('%s.hdr',fileprefix);
52 
+
53 
+      if ~exist(fn)
54 
+         msg = sprintf('Cannot find file "%s.hdr".', fileprefix);
55 
+         error(msg);
56 
+      end
57 
+   end
58 
+
59 
+   fid = fopen(fn,'r',machine);
60 
+
61 
+   if fid < 0,
62 
+      msg = sprintf('Cannot open file %s.',fn);
63 
+      error(msg);
64 
+   else
65 
+      hdr = read_header(fid);
66 
+      fclose(fid);
67 
+   end
68 
+
69 
+   if hdr.sizeof_hdr ~= 348
70 
+      % first try reading the opposite endian to 'machine'
71 
+      switch machine,
72 
+      case 'ieee-le', machine = 'ieee-be';
73 
+      case 'ieee-be', machine = 'ieee-le';
74 
+      end
75 
+
76 
+      fid = fopen(fn,'r',machine);
77 
+
78 
+      if fid < 0,
79 
+         msg = sprintf('Cannot open file %s.',fn);
80 
+         error(msg);
81 
+      else
82 
+         hdr = read_header(fid);
83 
+         fclose(fid);
84 
+      end
85 
+   end
86 
+
87 
+   if hdr.sizeof_hdr ~= 348
88 
+      % Now throw an error
89 
+      msg = sprintf('File "%s" is corrupted.',fn);
90 
+      error(msg);
91 
+   end
92 
+
93 
+   total_scan = hdr.dim(5);
94 
+
95 
+   return;					% get_nii_frame
96 
+
97 
+
98 
+%---------------------------------------------------------------------
99 
+function [ dsr ] = read_header(fid)
100 
+
101 
+    fseek(fid,0,'bof');
102 
+    dsr.sizeof_hdr    = fread(fid,1,'int32')';  % should be 348!
103 
+
104 
+    fseek(fid,40,'bof');
105 
+    dsr.dim           = fread(fid,8,'int16')';
106 
+
107 
+    return;					% read_header
108 
+
NIFTI_20090325/gpl.txt
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,230 @@
1 
+		        GNU GENERAL PUBLIC LICENSE
2 
+		           Version 2, June 1991
3 
+
4 
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
5 
+                       59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
6 
+ Everyone is permitted to copy and distribute verbatim copies
7 
+ of this license document, but changing it is not allowed.
8 
+
9 
+		    GNU GENERAL PUBLIC LICENSE
10 
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
11 
+
12 
+  0. This License applies to any program or other work which contains
13 
+a notice placed by the copyright holder saying it may be distributed
14 
+under the terms of this General Public License.  The "Program", below,
15 
+refers to any such program or work, and a "work based on the Program"
16 
+means either the Program or any derivative work under copyright law:
17 
+that is to say, a work containing the Program or a portion of it,
18 
+either verbatim or with modifications and/or translated into another
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+language.  (Hereinafter, translation is included without limitation in
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+the term "modification".)  Each licensee is addressed as "you".
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+
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+Activities other than copying, distribution and modification are not
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+covered by this License; they are outside its scope.  The act of
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+running the Program is not restricted, and the output from the Program
25 
+is covered only if its contents constitute a work based on the
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+Program (independent of having been made by running the Program).
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+Whether that is true depends on what the Program does.
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+  1. You may copy and distribute verbatim copies of the Program's
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+source code as you receive it, in any medium, provided that you
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+conspicuously and appropriately publish on each copy an appropriate
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+notices that refer to this License and to the absence of any warranty;
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+along with the Program.
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+
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+You may charge a fee for the physical act of transferring a copy, and
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+  2. You may modify your copy or copies of the Program or any portion
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+of it, thus forming a work based on the Program, and copy and
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+distribute such modifications or work under the terms of Section 1
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+above, provided that you also meet all of these conditions:
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+    a) You must cause the modified files to carry prominent notices
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+
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+These requirements apply to the modified work as a whole.  If
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+and can be reasonably considered independent and separate works in
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+distribute the same sections as part of a whole which is a work based
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+exercise the right to control the distribution of derivative or
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+In addition, mere aggregation of another work not based on the Program
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+with the Program (or with a work based on the Program) on a volume of
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+a storage or distribution medium does not bring the other work under
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+  3. You may copy and distribute the Program (or a work based on it,
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+under Section 2) in object code or executable form under the terms of
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+compelled to copy the source along with the object code.
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+
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+  4. You may not copy, modify, sublicense, or distribute the Program
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+except as expressly provided under this License.  Any attempt
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+otherwise to copy, modify, sublicense or distribute the Program is
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+void, and will automatically terminate your rights under this License.
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+However, parties who have received copies, or rights, from you under
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+this License will not have their licenses terminated so long as such
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+distribute the Program or its derivative works.  These actions are
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+prohibited by law if you do not accept this License.  Therefore, by
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+modifying or distributing the Program (or any work based on the
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+the Program or works based on it.
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+  6. Each time you redistribute the Program (or any work based on the
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+original licensor to copy, distribute or modify the Program subject to
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+these terms and conditions.  You may not impose any further
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+restrictions on the recipients' exercise of the rights granted herein.
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+You are not responsible for enforcing compliance by third parties to
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+  7. If, as a consequence of a court judgment or allegation of patent
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+conditions are imposed on you (whether by court order, agreement or
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+If any portion of this section is held invalid or unenforceable under
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+It is not the purpose of this section to induce you to infringe any
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+This section is intended to make thoroughly clear what is believed to
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+  8. If the distribution and/or use of the Program is restricted in
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+original copyright holder who places the Program under this License
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+  9. The Free Software Foundation may publish revised and/or new versions
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+Each version is given a distinguishing version number.  If the Program
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+later version", you have the option of following the terms and conditions
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+either of that version or of any later version published by the Free
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+Software Foundation.  If the Program does not specify a version number of
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+this License, you may choose any version ever published by the Free Software
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+Foundation.
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+  10. If you wish to incorporate parts of the Program into other free
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+of preserving the free status of all derivatives of our free software and
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+of promoting the sharing and reuse of software generally.
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+
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+			    NO WARRANTY
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+
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+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
211 
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
212 
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
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+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
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+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
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+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
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+
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+  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
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+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
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+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
223 
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
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+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
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+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
226 
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
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+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
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+POSSIBILITY OF SUCH DAMAGES.
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+
230 
+		     END OF TERMS AND CONDITIONS
NIFTI_20090325/load_nii.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,138 @@
1 
+%  Load NIFTI or ANALYZE dataset. Support both *.nii and *.hdr/*.img
2 
+%  file extension. If file extension is not provided, *.hdr/*.img will
3 
+%  be used as default.
4 
+%
5 
+%  A subset of NIFTI transform is included. For non-orthogonal rotation,
6 
+%  shearing etc., please use 'reslice_nii.m' to reslice the NIFTI file.
7 
+%  It will not cause negative effect, as long as you remember not to do
8 
+%  slice time correction after reslicing the NIFTI file. Output variable
9 
+%  nii will be in RAS orientation, i.e. X axis from Left to Right,
10 
+%  Y axis from Posterior to Anterior, and Z axis from Inferior to
11 
+%  Superior.
12 
+%
13 
+%  Usage: nii = load_nii(filename, [img_idx], [dim5_idx], [dim6_idx], ...
14 
+%			[dim7_idx], [old_RGB], [tolerance], [preferredForm])
15 
+%
16 
+%  filename  - 	NIFTI or ANALYZE file name.
17 
+%
18 
+%  img_idx (optional)  -  a numerical array of 4th dimension indices,
19 
+%	which is the indices of image scan volume. The number of images
20 
+%	scan volumes can be obtained from get_nii_frame.m, or simply
21 
+%	hdr.dime.dim(5). Only the specified volumes will be loaded.
22 
+%	All available image volumes will be loaded, if it is default or
23 
+%	empty.
24 
+%
25 
+%  dim5_idx (optional)  -  a numerical array of 5th dimension indices.
26 
+%	Only the specified range will be loaded. All available range
27 
+%	will be loaded, if it is default or empty.
28 
+%
29 
+%  dim6_idx (optional)  -  a numerical array of 6th dimension indices.
30 
+%	Only the specified range will be loaded. All available range
31 
+%	will be loaded, if it is default or empty.
32 
+%
33 
+%  dim7_idx (optional)  -  a numerical array of 7th dimension indices.
34 
+%	Only the specified range will be loaded. All available range
35 
+%	will be loaded, if it is default or empty.
36 
+%
37 
+%  old_RGB (optional)  -  a scale number to tell difference of new RGB24
38 
+%	from old RGB24. New RGB24 uses RGB triple sequentially for each
39 
+%	voxel, like [R1 G1 B1 R2 G2 B2 ...]. Analyze 6.0 from AnalyzeDirect
40 
+%	uses old RGB24, in a way like [R1 R2 ... G1 G2 ... B1 B2 ...] for
41 
+%	each slices. If the image that you view is garbled, try to set
42 
+%	old_RGB variable to 1 and try again, because it could be in
43 
+%	old RGB24. It will be set to 0, if it is default or empty.
44 
+%
45 
+%  tolerance (optional) - distortion allowed in the loaded image for any
46 
+%	non-orthogonal rotation or shearing of NIfTI affine matrix. If
47 
+%	you set 'tolerance' to 0, it means that you do not allow any
48 
+%	distortion. If you set 'tolerance' to 1, it means that you do
49 
+%	not care any distortion. The image will fail to be loaded if it
50 
+%	can not be tolerated. The tolerance will be set to 0.1 (10%), if
51 
+%	it is default or empty.
52 
+%
53 
+%  preferredForm (optional)  -  selects which transformation from voxels
54 
+%	to RAS coordinates; values are s,q,S,Q.  Lower case s,q indicate
55 
+%	"prefer sform or qform, but use others if preferred not present".
56 
+%	Upper case indicate the program is forced to use the specificied
57 
+%	tranform or fail loading.  'preferredForm' will be 's', if it is
58 
+%	default or empty.	- Jeff Gunter
59 
+%
60 
+%  Returned values:
61 
+%
62 
+%  nii structure:
63 
+%
64 
+%	hdr -		struct with NIFTI header fields.
65 
+%
66 
+%	filetype -	Analyze format .hdr/.img (0);
67 
+%			NIFTI .hdr/.img (1);
68 
+%			NIFTI .nii (2)
69 
+%
70 
+%	fileprefix - 	NIFTI filename without extension.
71 
+%
72 
+%	machine - 	machine string variable.
73 
+%
74 
+%	img - 		3D (or 4D) matrix of NIFTI data.
75 
+%
76 
+%	original -	the original header before any affine transform.
77 
+%
78 
+%  Part of this file is copied and modified under GNU license from
79 
+%  MRI_TOOLBOX developed by CNSP in Flinders University, Australia
80 
+%
81 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
82 
+%
83 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
84 
+%
85 
+function nii = load_nii(filename, img_idx, dim5_idx, dim6_idx, dim7_idx, ...
86 
+			old_RGB, tolerance, preferredForm)
87 
+
88 
+   if ~exist('filename','var')
89 
+      error('Usage: nii = load_nii(filename, [img_idx], [dim5_idx], [dim6_idx], [dim7_idx], [old_RGB], [tolerance], [preferredForm])');
90 
+   end
91 
+
92 
+   if ~exist('img_idx','var') | isempty(img_idx)
93 
+      img_idx = [];
94 
+   end
95 
+
96 
+   if ~exist('dim5_idx','var') | isempty(dim5_idx)
97 
+      dim5_idx = [];
98 
+   end
99 
+
100 
+   if ~exist('dim6_idx','var') | isempty(dim6_idx)
101 
+      dim6_idx = [];
102 
+   end
103 
+
104 
+   if ~exist('dim7_idx','var') | isempty(dim7_idx)
105 
+      dim7_idx = [];
106 
+   end
107 
+
108 
+   if ~exist('old_RGB','var') | isempty(old_RGB)
109 
+      old_RGB = 0;
110 
+   end
111 
+
112 
+   if ~exist('tolerance','var') | isempty(tolerance)
113 
+      tolerance = 0.1;			% 10 percent
114 
+   end
115 
+
116 
+   if ~exist('preferredForm','var') | isempty(preferredForm)
117 
+      preferredForm= 's';		% Jeff
118 
+   end
119 
+
120 
+   %  Read the dataset header
121 
+   %
122 
+   [nii.hdr,nii.filetype,nii.fileprefix,nii.machine] = load_nii_hdr(filename);
123 
+
124 
+   %  Read the header extension
125 
+   %
126 
+%   nii.ext = load_nii_ext(filename);
127 
+
128 
+   %  Read the dataset body
129 
+   %
130 
+   [nii.img,nii.hdr] = load_nii_img(nii.hdr,nii.filetype,nii.fileprefix, ...
131 
+		nii.machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB);
132 
+
133 
+   %  Perform some of sform/qform transform
134 
+   %
135 
+   nii = xform_nii(nii, tolerance, preferredForm);
136 
+
137 
+   return					% load_nii
138 
+
NIFTI_20090325/load_nii_ext.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,148 @@
1 
+%  Load NIFTI header extension after its header is loaded using load_nii_hdr.
2 
+%
3 
+%  Usage: ext = load_nii_ext(filename)
4 
+%
5 
+%  filename - NIFTI file name.
6 
+%
7 
+%  Returned values:
8 
+%
9 
+%  ext - Structure of NIFTI header extension, which includes num_ext,
10 
+%       and all the extended header sections in the header extension.
11 
+%       Each extended header section will have its esize, ecode, and
12 
+%       edata, where edata can be plain text, xml, or any raw data
13 
+%       that was saved in the extended header section.
14 
+%
15 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
16 
+%
17 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
18 
+%
19 
+function ext = load_nii_ext(fileprefix)
20 
+
21 
+   if ~exist('fileprefix','var'),
22 
+      error('Usage: ext = load_nii_ext(filename)');
23 
+   end
24 
+
25 
+   machine = 'ieee-le';
26 
+   new_ext = 0;
27 
+
28 
+   if findstr('.nii',fileprefix)
29 
+      new_ext = 1;
30 
+      fileprefix = strrep(fileprefix,'.nii','');
31 
+   end
32 
+
33 
+   if findstr('.hdr',fileprefix)
34 
+      fileprefix = strrep(fileprefix,'.hdr','');
35 
+   end
36 
+
37 
+   if findstr('.img',fileprefix)
38 
+      fileprefix = strrep(fileprefix,'.img','');
39 
+   end
40 
+
41 
+   if new_ext
42 
+      fn = sprintf('%s.nii',fileprefix);
43 
+
44 
+      if ~exist(fn)
45 
+         msg = sprintf('Cannot find file "%s.nii".', fileprefix);
46 
+         error(msg);
47 
+      end
48 
+   else
49 
+      fn = sprintf('%s.hdr',fileprefix);
50 
+
51 
+      if ~exist(fn)
52 
+         msg = sprintf('Cannot find file "%s.hdr".', fileprefix);
53 
+         error(msg);
54 
+      end
55 
+   end
56 
+
57 
+   fid = fopen(fn,'r',machine);
58 
+   vox_offset = 0;
59 
+
60 
+   if fid < 0,
61 
+      msg = sprintf('Cannot open file %s.',fn);
62 
+      error(msg);
63 
+   else
64 
+      fseek(fid,0,'bof');
65 
+
66 
+      if fread(fid,1,'int32') == 348
67 
+         if new_ext
68 
+            fseek(fid,108,'bof');
69 
+            vox_offset = fread(fid,1,'float32');
70 
+         end
71 
+
72 
+         ext = read_extension(fid, vox_offset);
73 
+         fclose(fid);
74 
+      else
75 
+         fclose(fid);
76 
+
77 
+         %  first try reading the opposite endian to 'machine'
78 
+         %
79 
+         switch machine,
80 
+         case 'ieee-le', machine = 'ieee-be';
81 
+         case 'ieee-be', machine = 'ieee-le';
82 
+         end
83 
+
84 
+         fid = fopen(fn,'r',machine);
85 
+
86 
+         if fid < 0,
87 
+            msg = sprintf('Cannot open file %s.',fn);
88 
+            error(msg);
89 
+         else
90 
+            fseek(fid,0,'bof');
91 
+
92 
+            if fread(fid,1,'int32') ~= 348
93 
+
94 
+               %  Now throw an error
95 
+               %
96 
+               msg = sprintf('File "%s" is corrupted.',fn);
97 
+               error(msg);
98 
+            end
99 
+
100 
+            if new_ext
101 
+               fseek(fid,108,'bof');
102 
+               vox_offset = fread(fid,1,'float32');
103 
+            end
104 
+
105 
+            ext = read_extension(fid, vox_offset);
106 
+            fclose(fid);
107 
+         end
108 
+      end
109 
+   end
110 
+
111 
+   return                                       % load_nii_ext
112 
+
113 
+
114 
+%---------------------------------------------------------------------
115 
+function ext = read_extension(fid, vox_offset)
116 
+
117 
+   ext = [];
118 
+
119 
+   if vox_offset
120 
+      end_of_ext = vox_offset;
121 
+   else
122 
+      fseek(fid, 0, 'eof');
123 
+      end_of_ext = ftell(fid);
124 
+   end
125 
+
126 
+   if end_of_ext > 352
127 
+      fseek(fid, 348, 'bof');
128 
+      ext.extension = fread(fid,4)';
129 
+   end
130 
+
131 
+   if isempty(ext) | ext.extension(1) == 0
132 
+      ext = [];
133 
+      return;
134 
+   end
135 
+
136 
+   i = 1;
137 
+
138 
+   while(ftell(fid) < end_of_ext)
139 
+      ext.section(i).esize = fread(fid,1,'int32');
140 
+      ext.section(i).ecode = fread(fid,1,'int32');
141 
+      ext.section(i).edata = char(fread(fid,ext.section(i).esize-8)');
142 
+      i = i + 1;
143 
+   end
144 
+
145 
+   ext.num_ext = length(ext.section);
146 
+
147 
+   return                                               % read_extension
148 
+
NIFTI_20090325/load_nii_hdr.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,320 @@
1 
+%  Load NIFTI dataset header. Support both *.nii and *.hdr/*.img file
2 
+%  extension. If file extension is not provided, *.hdr/*.img will be
3 
+%  used as default.
4 
+%
5 
+%  Usage: [hdr, filetype, fileprefix, machine] = load_nii_hdr(filename)
6 
+%
7 
+%  filename - NIFTI file name.
8 
+%
9 
+%  Returned values:
10 
+%
11 
+%  hdr - struct with NIFTI header fields.
12 
+%
13 
+%  filetype	- 0 for Analyze format (*.hdr/*.img);
14 
+%		  1 for NIFTI format in 2 files (*.hdr/*.img);
15 
+%		  2 for NIFTI format in 1 file (*.nii).
16 
+%
17 
+%  fileprefix - NIFTI file name without extension.
18 
+%
19 
+%  machine    - a string, see below for details. The default here is 'ieee-le'.
20 
+%
21 
+%    'native'      or 'n' - local machine format - the default
22 
+%    'ieee-le'     or 'l' - IEEE floating point with little-endian
23 
+%                           byte ordering
24 
+%    'ieee-be'     or 'b' - IEEE floating point with big-endian
25 
+%                           byte ordering
26 
+%    'vaxd'        or 'd' - VAX D floating point and VAX ordering
27 
+%    'vaxg'        or 'g' - VAX G floating point and VAX ordering
28 
+%    'cray'        or 'c' - Cray floating point with big-endian
29 
+%                           byte ordering
30 
+%    'ieee-le.l64' or 'a' - IEEE floating point with little-endian
31 
+%                           byte ordering and 64 bit long data type
32 
+%    'ieee-be.l64' or 's' - IEEE floating point with big-endian byte
33 
+%                           ordering and 64 bit long data type.
34 
+%
35 
+%  Number of scanned images in the file can be obtained by:
36 
+%  num_scan = hdr.dime.dim(5)
37 
+%
38 
+%  Part of this file is copied and modified under GNU license from
39 
+%  MRI_TOOLBOX developed by CNSP in Flinders University, Australia
40 
+%
41 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
42 
+%
43 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
44 
+%
45 
+function [hdr, filetype, fileprefix, machine] = load_nii_hdr(fileprefix)
46 
+
47 
+   if ~exist('fileprefix','var'),
48 
+      error('Usage: [hdr, filetype, fileprefix, machine] = load_nii_hdr(filename)');
49 
+   end
50 
+
51 
+   machine = 'ieee-le';
52 
+   new_ext = 0;
53 
+
54 
+   if findstr('.nii',fileprefix)
55 
+      new_ext = 1;
56 
+      fileprefix = strrep(fileprefix,'.nii','');
57 
+   end
58 
+
59 
+   if findstr('.hdr',fileprefix)
60 
+      fileprefix = strrep(fileprefix,'.hdr','');
61 
+   end
62 
+
63 
+   if findstr('.img',fileprefix)
64 
+      fileprefix = strrep(fileprefix,'.img','');
65 
+   end
66 
+
67 
+   if new_ext
68 
+      fn = sprintf('%s.nii',fileprefix);
69 
+
70 
+      if ~exist(fn)
71 
+         msg = sprintf('Cannot find file "%s.nii".', fileprefix);
72 
+         error(msg);
73 
+      end
74 
+   else
75 
+      fn = sprintf('%s.hdr',fileprefix);
76 
+
77 
+      if ~exist(fn)
78 
+         msg = sprintf('Cannot find file "%s.hdr".', fileprefix);
79 
+         error(msg);
80 
+      end
81 
+   end
82 
+
83 
+   fid = fopen(fn,'r',machine);
84 
+
85 
+   if fid < 0,
86 
+      msg = sprintf('Cannot open file %s.',fn);
87 
+      error(msg);
88 
+   else
89 
+      fseek(fid,0,'bof');
90 
+
91 
+      if fread(fid,1,'int32') == 348
92 
+         hdr = read_header(fid);
93 
+         fclose(fid);
94 
+      else
95 
+         fclose(fid);
96 
+
97 
+         %  first try reading the opposite endian to 'machine'
98 
+         %
99 
+         switch machine,
100 
+         case 'ieee-le', machine = 'ieee-be';
101 
+         case 'ieee-be', machine = 'ieee-le';
102 
+         end
103 
+
104 
+         fid = fopen(fn,'r',machine);
105 
+
106 
+         if fid < 0,
107 
+            msg = sprintf('Cannot open file %s.',fn);
108 
+            error(msg);
109 
+         else
110 
+            fseek(fid,0,'bof');
111 
+
112 
+            if fread(fid,1,'int32') ~= 348
113 
+
114 
+               %  Now throw an error
115 
+               %
116 
+               msg = sprintf('File "%s" is corrupted.',fn);
117 
+               error(msg);
118 
+            end
119 
+
120 
+            hdr = read_header(fid);
121 
+            fclose(fid);
122 
+         end
123 
+      end
124 
+   end
125 
+
126 
+   if strcmp(hdr.hist.magic, 'n+1')
127 
+      filetype = 2;
128 
+   elseif strcmp(hdr.hist.magic, 'ni1')
129 
+      filetype = 1;
130 
+   else
131 
+      filetype = 0;
132 
+   end
133 
+
134 
+   return					% load_nii_hdr
135 
+
136 
+
137 
+%---------------------------------------------------------------------
138 
+function [ dsr ] = read_header(fid)
139 
+
140 
+        %  Original header structures
141 
+	%  struct dsr
142 
+	%       {
143 
+	%       struct header_key hk;            /*   0 +  40       */
144 
+	%       struct image_dimension dime;     /*  40 + 108       */
145 
+	%       struct data_history hist;        /* 148 + 200       */
146 
+	%       };                               /* total= 348 bytes*/
147 
+
148 
+    dsr.hk   = header_key(fid);
149 
+    dsr.dime = image_dimension(fid);
150 
+    dsr.hist = data_history(fid);
151 
+
152 
+    %  For Analyze data format
153 
+    %
154 
+    if ~strcmp(dsr.hist.magic, 'n+1') & ~strcmp(dsr.hist.magic, 'ni1')
155 
+        dsr.hist.qform_code = 0;
156 
+        dsr.hist.sform_code = 0;
157 
+    end
158 
+
159 
+    return					% read_header
160 
+
161 
+
162 
+%---------------------------------------------------------------------
163 
+function [ hk ] = header_key(fid)
164 
+
165 
+    fseek(fid,0,'bof');
166 
+
167 
+	%  Original header structures
168 
+	%  struct header_key                     /* header key      */
169 
+	%       {                                /* off + size      */
170 
+	%       int sizeof_hdr                   /*  0 +  4         */
171 
+	%       char data_type[10];              /*  4 + 10         */
172 
+	%       char db_name[18];                /* 14 + 18         */
173 
+	%       int extents;                     /* 32 +  4         */
174 
+	%       short int session_error;         /* 36 +  2         */
175 
+	%       char regular;                    /* 38 +  1         */
176 
+	%       char dim_info;   % char hkey_un0;        /* 39 +  1 */
177 
+	%       };                               /* total=40 bytes  */
178 
+	%
179 
+	% int sizeof_header   Should be 348.
180 
+	% char regular        Must be 'r' to indicate that all images and
181 
+	%                     volumes are the same size.
182 
+
183 
+    v6 = version;
184 
+    if str2num(v6(1))<6
185 
+       directchar = '*char';
186 
+    else
187 
+       directchar = 'uchar=>char';
188 
+    end
189 
+
190 
+    hk.sizeof_hdr    = fread(fid, 1,'int32')';	% should be 348!
191 
+    hk.data_type     = deblank(fread(fid,10,directchar)');
192 
+    hk.db_name       = deblank(fread(fid,18,directchar)');
193 
+    hk.extents       = fread(fid, 1,'int32')';
194 
+    hk.session_error = fread(fid, 1,'int16')';
195 
+    hk.regular       = fread(fid, 1,directchar)';
196 
+    hk.dim_info      = fread(fid, 1,'uchar')';
197 
+
198 
+    return					% header_key
199 
+
200 
+
201 
+%---------------------------------------------------------------------
202 
+function [ dime ] = image_dimension(fid)
203 
+
204 
+	%  Original header structures
205 
+	%  struct image_dimension
206 
+	%       {                                /* off + size      */
207 
+	%       short int dim[8];                /* 0 + 16          */
208 
+        %       /*
209 
+        %           dim[0]      Number of dimensions in database; usually 4.
210 
+        %           dim[1]      Image X dimension;  number of *pixels* in an image row.
211 
+        %           dim[2]      Image Y dimension;  number of *pixel rows* in slice.
212 
+        %           dim[3]      Volume Z dimension; number of *slices* in a volume.
213 
+        %           dim[4]      Time points; number of volumes in database
214 
+        %       */
215 
+	%       float intent_p1;   % char vox_units[4];   /* 16 + 4       */
216 
+	%       float intent_p2;   % char cal_units[8];   /* 20 + 4       */
217 
+	%       float intent_p3;   % char cal_units[8];   /* 24 + 4       */
218 
+	%       short int intent_code;   % short int unused1;   /* 28 + 2 */
219 
+	%       short int datatype;              /* 30 + 2          */
220 
+	%       short int bitpix;                /* 32 + 2          */
221 
+	%       short int slice_start;   % short int dim_un0;   /* 34 + 2 */
222 
+	%       float pixdim[8];                 /* 36 + 32         */
223 
+	%	/*
224 
+	%		pixdim[] specifies the voxel dimensions:
225 
+	%		pixdim[1] - voxel width, mm
226 
+	%		pixdim[2] - voxel height, mm
227 
+	%		pixdim[3] - slice thickness, mm
228 
+	%		pixdim[4] - volume timing, in msec
229 
+	%					..etc
230 
+	%	*/
231 
+	%       float vox_offset;                /* 68 + 4          */
232 
+	%       float scl_slope;   % float roi_scale;     /* 72 + 4 */
233 
+	%       float scl_inter;   % float funused1;      /* 76 + 4 */
234 
+	%       short slice_end;   % float funused2;      /* 80 + 2 */
235 
+	%       char slice_code;   % float funused2;      /* 82 + 1 */
236 
+	%       char xyzt_units;   % float funused2;      /* 83 + 1 */
237 
+	%       float cal_max;                   /* 84 + 4          */
238 
+	%       float cal_min;                   /* 88 + 4          */
239 
+	%       float slice_duration;   % int compressed; /* 92 + 4 */
240 
+	%       float toffset;   % int verified;          /* 96 + 4 */
241 
+	%       int glmax;                       /* 100 + 4         */
242 
+	%       int glmin;                       /* 104 + 4         */
243 
+	%       };                               /* total=108 bytes */
244 
+
245 
+    dime.dim        = fread(fid,8,'int16')';
246 
+    dime.intent_p1  = fread(fid,1,'float32')';
247 
+    dime.intent_p2  = fread(fid,1,'float32')';
248 
+    dime.intent_p3  = fread(fid,1,'float32')';
249 
+    dime.intent_code = fread(fid,1,'int16')';
250 
+    dime.datatype   = fread(fid,1,'int16')';
251 
+    dime.bitpix     = fread(fid,1,'int16')';
252 
+    dime.slice_start = fread(fid,1,'int16')';
253 
+    dime.pixdim     = abs(fread(fid,8,'float32')');
254 
+    dime.vox_offset = fread(fid,1,'float32')';
255 
+    dime.scl_slope  = fread(fid,1,'float32')';
256 
+    dime.scl_inter  = fread(fid,1,'float32')';
257 
+    dime.slice_end  = fread(fid,1,'int16')';
258 
+    dime.slice_code = fread(fid,1,'uchar')';
259 
+    dime.xyzt_units = fread(fid,1,'uchar')';
260 
+    dime.cal_max    = fread(fid,1,'float32')';
261 
+    dime.cal_min    = fread(fid,1,'float32')';
262 
+    dime.slice_duration = fread(fid,1,'float32')';
263 
+    dime.toffset    = fread(fid,1,'float32')';
264 
+    dime.glmax      = fread(fid,1,'int32')';
265 
+    dime.glmin      = fread(fid,1,'int32')';
266 
+
267 
+    return					% image_dimension
268 
+
269 
+
270 
+%---------------------------------------------------------------------
271 
+function [ hist ] = data_history(fid)
272 
+
273 
+	%  Original header structures
274 
+	%  struct data_history
275 
+	%       {                                /* off + size      */
276 
+	%       char descrip[80];                /* 0 + 80          */
277 
+	%       char aux_file[24];               /* 80 + 24         */
278 
+	%       short int qform_code;            /* 104 + 2         */
279 
+	%       short int sform_code;            /* 106 + 2         */
280 
+	%       float quatern_b;                 /* 108 + 4         */
281 
+	%       float quatern_c;                 /* 112 + 4         */
282 
+	%       float quatern_d;                 /* 116 + 4         */
283 
+	%       float qoffset_x;                 /* 120 + 4         */
284 
+	%       float qoffset_y;                 /* 124 + 4         */
285 
+	%       float qoffset_z;                 /* 128 + 4         */
286 
+	%       float srow_x[4];                 /* 132 + 16        */
287 
+	%       float srow_y[4];                 /* 148 + 16        */
288 
+	%       float srow_z[4];                 /* 164 + 16        */
289 
+	%       char intent_name[16];            /* 180 + 16        */
290 
+	%       char magic[4];   % int smin;     /* 196 + 4         */
291 
+	%       };                               /* total=200 bytes */
292 
+
293 
+    v6 = version;
294 
+    if str2num(v6(1))<6
295 
+       directchar = '*char';
296 
+    else
297 
+       directchar = 'uchar=>char';
298 
+    end
299 
+
300 
+    hist.descrip     = deblank(fread(fid,80,directchar)');
301 
+    hist.aux_file    = deblank(fread(fid,24,directchar)');
302 
+    hist.qform_code  = fread(fid,1,'int16')';
303 
+    hist.sform_code  = fread(fid,1,'int16')';
304 
+    hist.quatern_b   = fread(fid,1,'float32')';
305 
+    hist.quatern_c   = fread(fid,1,'float32')';
306 
+    hist.quatern_d   = fread(fid,1,'float32')';
307 
+    hist.qoffset_x   = fread(fid,1,'float32')';
308 
+    hist.qoffset_y   = fread(fid,1,'float32')';
309 
+    hist.qoffset_z   = fread(fid,1,'float32')';
310 
+    hist.srow_x      = fread(fid,4,'float32')';
311 
+    hist.srow_y      = fread(fid,4,'float32')';
312 
+    hist.srow_z      = fread(fid,4,'float32')';
313 
+    hist.intent_name = deblank(fread(fid,16,directchar)');
314 
+    hist.magic       = deblank(fread(fid,4,directchar)');
315 
+
316 
+    fseek(fid,253,'bof');
317 
+    hist.originator  = fread(fid, 5,'int16')';
318 
+
319 
+    return					% data_history
320 
+
NIFTI_20090325/load_nii_img.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,385 @@
1 
+%  internal function
2 
+
3 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
4 
+
5 
+function [img,hdr] = load_nii_img(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB)
6 
+
7 
+   if ~exist('hdr','var') | ~exist('filetype','var') | ~exist('fileprefix','var') | ~exist('machine','var')
8 
+      error('Usage: [img,hdr] = load_nii_img(hdr,filetype,fileprefix,machine,[img_idx],[dim5_idx],[dim6_idx],[dim7_idx],[old_RGB]);');
9 
+   end
10 
+
11 
+   if ~exist('img_idx','var') | isempty(img_idx) | hdr.dime.dim(5)<1
12 
+      img_idx = [];
13 
+   end
14 
+
15 
+   if ~exist('dim5_idx','var') | isempty(dim5_idx) | hdr.dime.dim(6)<1
16 
+      dim5_idx = [];
17 
+   end
18 
+
19 
+   if ~exist('dim6_idx','var') | isempty(dim6_idx) | hdr.dime.dim(7)<1
20 
+      dim6_idx = [];
21 
+   end
22 
+
23 
+   if ~exist('dim7_idx','var') | isempty(dim7_idx) | hdr.dime.dim(8)<1
24 
+      dim7_idx = [];
25 
+   end
26 
+
27 
+   if ~exist('old_RGB','var') | isempty(old_RGB)
28 
+      old_RGB = 0;
29 
+   end
30 
+
31 
+   %  check img_idx
32 
+   %
33 
+   if ~isempty(img_idx) & ~isnumeric(img_idx)
34 
+      error('"img_idx" should be a numerical array.');
35 
+   end
36 
+
37 
+   if length(unique(img_idx)) ~= length(img_idx)
38 
+      error('Duplicate image index in "img_idx"');
39 
+   end
40 
+
41 
+   if ~isempty(img_idx) & (min(img_idx) < 1 | max(img_idx) > hdr.dime.dim(5))
42 
+      max_range = hdr.dime.dim(5);
43 
+
44 
+      if max_range == 1
45 
+         error(['"img_idx" should be 1.']);
46 
+      else
47 
+         range = ['1 ' num2str(max_range)];
48 
+         error(['"img_idx" should be an integer within the range of [' range '].']);
49 
+      end
50 
+   end
51 
+
52 
+   %  check dim5_idx
53 
+   %
54 
+   if ~isempty(dim5_idx) & ~isnumeric(dim5_idx)
55 
+      error('"dim5_idx" should be a numerical array.');
56 
+   end
57 
+
58 
+   if length(unique(dim5_idx)) ~= length(dim5_idx)
59 
+      error('Duplicate image index in "dim5_idx"');
60 
+   end
61 
+
62 
+   if ~isempty(dim5_idx) & (min(dim5_idx) < 1 | max(dim5_idx) > hdr.dime.dim(6))
63 
+      max_range = hdr.dime.dim(6);
64 
+
65 
+      if max_range == 1
66 
+         error(['"dim5_idx" should be 1.']);
67 
+      else
68 
+         range = ['1 ' num2str(max_range)];
69 
+         error(['"dim5_idx" should be an integer within the range of [' range '].']);
70 
+      end
71 
+   end
72 
+
73 
+   %  check dim6_idx
74 
+   %
75 
+   if ~isempty(dim6_idx) & ~isnumeric(dim6_idx)
76 
+      error('"dim6_idx" should be a numerical array.');
77 
+   end
78 
+
79 
+   if length(unique(dim6_idx)) ~= length(dim6_idx)
80 
+      error('Duplicate image index in "dim6_idx"');
81 
+   end
82 
+
83 
+   if ~isempty(dim6_idx) & (min(dim6_idx) < 1 | max(dim6_idx) > hdr.dime.dim(7))
84 
+      max_range = hdr.dime.dim(7);
85 
+
86 
+      if max_range == 1
87 
+         error(['"dim6_idx" should be 1.']);
88 
+      else
89 
+         range = ['1 ' num2str(max_range)];
90 
+         error(['"dim6_idx" should be an integer within the range of [' range '].']);
91 
+      end
92 
+   end
93 
+
94 
+   %  check dim7_idx
95 
+   %
96 
+   if ~isempty(dim7_idx) & ~isnumeric(dim7_idx)
97 
+      error('"dim7_idx" should be a numerical array.');
98 
+   end
99 
+
100 
+   if length(unique(dim7_idx)) ~= length(dim7_idx)
101 
+      error('Duplicate image index in "dim7_idx"');
102 
+   end
103 
+
104 
+   if ~isempty(dim7_idx) & (min(dim7_idx) < 1 | max(dim7_idx) > hdr.dime.dim(8))
105 
+      max_range = hdr.dime.dim(8);
106 
+
107 
+      if max_range == 1
108 
+         error(['"dim7_idx" should be 1.']);
109 
+      else
110 
+         range = ['1 ' num2str(max_range)];
111 
+         error(['"dim7_idx" should be an integer within the range of [' range '].']);
112 
+      end
113 
+   end
114 
+
115 
+   [img,hdr] = read_image(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB);
116 
+
117 
+   return					% load_nii_img
118 
+
119 
+
120 
+%---------------------------------------------------------------------
121 
+function [img,hdr] = read_image(hdr, filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB)
122 
+
123 
+   switch filetype
124 
+   case {0, 1}
125 
+      fn = [fileprefix '.img'];
126 
+   case 2
127 
+      fn = [fileprefix '.nii'];
128 
+   end
129 
+
130 
+   fid = fopen(fn,'r',machine);
131 
+
132 
+   if fid < 0,
133 
+      msg = sprintf('Cannot open file %s.',fn);
134 
+      error(msg);
135 
+   end
136 
+
137 
+   %  Set bitpix according to datatype
138 
+   %
139 
+   %  /*Acceptable values for datatype are*/
140 
+   %
141 
+   %     0 None                     (Unknown bit per voxel) % DT_NONE, DT_UNKNOWN
142 
+   %     1 Binary                         (ubit1, bitpix=1) % DT_BINARY
143 
+   %     2 Unsigned char         (uchar or uint8, bitpix=8) % DT_UINT8, NIFTI_TYPE_UINT8
144 
+   %     4 Signed short                  (int16, bitpix=16) % DT_INT16, NIFTI_TYPE_INT16
145 
+   %     8 Signed integer                (int32, bitpix=32) % DT_INT32, NIFTI_TYPE_INT32
146 
+   %    16 Floating point    (single or float32, bitpix=32) % DT_FLOAT32, NIFTI_TYPE_FLOAT32
147 
+   %    32 Complex, 2 float32      (Use float32, bitpix=64) % DT_COMPLEX64, NIFTI_TYPE_COMPLEX64
148 
+   %    64 Double precision  (double or float64, bitpix=64) % DT_FLOAT64, NIFTI_TYPE_FLOAT64
149 
+   %   128 uint8 RGB                 (Use uint8, bitpix=24) % DT_RGB24, NIFTI_TYPE_RGB24
150 
+   %   256 Signed char            (schar or int8, bitpix=8) % DT_INT8, NIFTI_TYPE_INT8
151 
+   %   511 Single RGB              (Use float32, bitpix=96) % DT_RGB96, NIFTI_TYPE_RGB96
152 
+   %   512 Unsigned short               (uint16, bitpix=16) % DT_UNINT16, NIFTI_TYPE_UNINT16
153 
+   %   768 Unsigned integer             (uint32, bitpix=32) % DT_UNINT32, NIFTI_TYPE_UNINT32
154 
+   %  1024 Signed long long              (int64, bitpix=64) % DT_INT64, NIFTI_TYPE_INT64
155 
+   %  1280 Unsigned long long           (uint64, bitpix=64) % DT_UINT64, NIFTI_TYPE_UINT64
156 
+   %  1536 Long double, float128  (Unsupported, bitpix=128) % DT_FLOAT128, NIFTI_TYPE_FLOAT128
157 
+   %  1792 Complex128, 2 float64  (Use float64, bitpix=128) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128
158 
+   %  2048 Complex256, 2 float128 (Unsupported, bitpix=256) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128
159 
+   %
160 
+   switch hdr.dime.datatype
161 
+   case   1,
162 
+      hdr.dime.bitpix = 1;  precision = 'ubit1';
163 
+   case   2,
164 
+      hdr.dime.bitpix = 8;  precision = 'uint8';
165 
+   case   4,
166 
+      hdr.dime.bitpix = 16; precision = 'int16';
167 
+   case   8,
168 
+      hdr.dime.bitpix = 32; precision = 'int32';
169 
+   case  16,
170 
+      hdr.dime.bitpix = 32; precision = 'float32';
171 
+   case  32,
172 
+      hdr.dime.bitpix = 64; precision = 'float32';
173 
+   case  64,
174 
+      hdr.dime.bitpix = 64; precision = 'float64';
175 
+   case 128,
176 
+      hdr.dime.bitpix = 24; precision = 'uint8';
177 
+   case 256
178 
+      hdr.dime.bitpix = 8;  precision = 'int8';
179 
+   case 511
180 
+      hdr.dime.bitpix = 96; precision = 'float32';
181 
+   case 512
182 
+      hdr.dime.bitpix = 16; precision = 'uint16';
183 
+   case 768
184 
+      hdr.dime.bitpix = 32; precision = 'uint32';
185 
+   case 1024
186 
+      hdr.dime.bitpix = 64; precision = 'int64';
187 
+   case 1280
188 
+      hdr.dime.bitpix = 64; precision = 'uint64';
189 
+   case 1792,
190 
+      hdr.dime.bitpix = 128; precision = 'float64';
191 
+   otherwise
192 
+      error('This datatype is not supported');
193 
+   end
194 
+
195 
+   hdr.dime.dim(find(hdr.dime.dim < 1)) = 1;
196 
+
197 
+   %  move pointer to the start of image block
198 
+   %
199 
+   switch filetype
200 
+   case {0, 1}
201 
+      fseek(fid, 0, 'bof');
202 
+   case 2
203 
+      fseek(fid, hdr.dime.vox_offset, 'bof');
204 
+   end
205 
+
206 
+   %  Load whole image block for old Analyze format or binary image;
207 
+   %  otherwise, load images that are specified in img_idx, dim5_idx,
208 
+   %  dim6_idx, and dim7_idx
209 
+   %
210 
+   %  For binary image, we have to read all because pos can not be
211 
+   %  seeked in bit and can not be calculated the way below.
212 
+   %
213 
+   if filetype == 0 | hdr.dime.datatype == 1 | isequal(hdr.dime.dim(5:8),ones(1,4)) | ...
214 
+	(isempty(img_idx) & isempty(dim5_idx) & isempty(dim6_idx) & isempty(dim7_idx))
215 
+
216 
+      %  For each frame, precision of value will be read
217 
+      %  in img_siz times, where img_siz is only the
218 
+      %  dimension size of an image, not the byte storage
219 
+      %  size of an image.
220 
+      %
221 
+      img_siz = prod(hdr.dime.dim(2:8));
222 
+
223 
+      %  For complex float32 or complex float64, voxel values
224 
+      %  include [real, imag]
225 
+      %
226 
+      if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
227 
+         img_siz = img_siz * 2;
228 
+      end
229 
+
230 
+      %MPH: For RGB24, voxel values include 3 separate color planes
231 
+      %
232 
+      if hdr.dime.datatype == 128 | hdr.dime.datatype == 511
233 
+	 img_siz = img_siz * 3;
234 
+      end
235 
+
236 
+      img = fread(fid, img_siz, sprintf('*%s',precision));
237 
+
238 
+      d1 = hdr.dime.dim(2);
239 
+      d2 = hdr.dime.dim(3);
240 
+      d3 = hdr.dime.dim(4);
241 
+      d4 = hdr.dime.dim(5);
242 
+      d5 = hdr.dime.dim(6);
243 
+      d6 = hdr.dime.dim(7);
244 
+      d7 = hdr.dime.dim(8);
245 
+
246 
+      if isempty(img_idx)
247 
+         img_idx = 1:d4;
248 
+      end
249 
+
250 
+      if isempty(dim5_idx)
251 
+         dim5_idx = 1:d5;
252 
+      end
253 
+
254 
+      if isempty(dim6_idx)
255 
+         dim6_idx = 1:d6;
256 
+      end
257 
+
258 
+      if isempty(dim7_idx)
259 
+         dim7_idx = 1:d7;
260 
+      end
261 
+   else
262 
+
263 
+      img = [];
264 
+
265 
+      %  For each frame, precision of value will be read
266 
+      %  in img_siz times, where img_siz is only the
267 
+      %  dimension size of an image, not the byte storage
268 
+      %  size of an image.
269 
+      %
270 
+      img_siz = prod(hdr.dime.dim(2:4));
271 
+
272 
+      d1 = hdr.dime.dim(2);
273 
+      d2 = hdr.dime.dim(3);
274 
+      d3 = hdr.dime.dim(4);
275 
+      d4 = hdr.dime.dim(5);
276 
+      d5 = hdr.dime.dim(6);
277 
+      d6 = hdr.dime.dim(7);
278 
+      d7 = hdr.dime.dim(8);
279 
+
280 
+      if isempty(img_idx)
281 
+         img_idx = 1:d4;
282 
+      end
283 
+
284 
+      if isempty(dim5_idx)
285 
+         dim5_idx = 1:d5;
286 
+      end
287 
+
288 
+      if isempty(dim6_idx)
289 
+         dim6_idx = 1:d6;
290 
+      end
291 
+
292 
+      if isempty(dim7_idx)
293 
+         dim7_idx = 1:d7;
294 
+      end
295 
+
296 
+      for i7=1:length(dim7_idx)
297 
+         for i6=1:length(dim6_idx)
298 
+            for i5=1:length(dim5_idx)
299 
+               for t=1:length(img_idx)
300 
+
301 
+                  %  Position is seeked in bytes. To convert dimension size
302 
+                  %  to byte storage size, hdr.dime.bitpix/8 will be
303 
+                  %  applied.
304 
+                  %
305 
+                  pos = sub2ind([d1 d2 d3 d4 d5 d6 d7], 1, 1, 1, ...
306 
+			img_idx(t), dim5_idx(i5),dim6_idx(i6),dim7_idx(i7)) -1;
307 
+                  pos = pos * hdr.dime.bitpix/8;
308 
+
309 
+                  %  For complex float32 or complex float64, voxel values
310 
+                  %  include [real, imag]
311 
+                  %
312 
+                  if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
313 
+                     img_siz = img_siz * 2;
314 
+                  end
315 
+
316 
+                  %MPH: For RGB24, voxel values include 3 separate color planes
317 
+                  %
318 
+                  if hdr.dime.datatype == 128 | hdr.dime.datatype == 511
319 
+	             img_siz = img_siz * 3;
320 
+                  end
321 
+
322 
+                  if filetype == 2
323 
+                     fseek(fid, pos + hdr.dime.vox_offset, 'bof');
324 
+                  else
325 
+                     fseek(fid, pos, 'bof');
326 
+                  end
327 
+
328 
+                  %  For each frame, fread will read precision of value
329 
+                  %  in img_siz times
330 
+                  %
331 
+                  img = [img fread(fid, img_siz, sprintf('*%s',precision))];
332 
+               end
333 
+            end
334 
+         end
335 
+      end
336 
+   end
337 
+
338 
+   %  For complex float32 or complex float64, voxel values
339 
+   %  include [real, imag]
340 
+   %
341 
+   if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
342 
+      img = reshape(img, [2, length(img)/2]);
343 
+      img = complex(img(1,:)', img(2,:)');
344 
+   end
345 
+
346 
+   fclose(fid);
347 
+
348 
+   %  Update the global min and max values
349 
+   %
350 
+   hdr.dime.glmax = max(double(img(:)));
351 
+   hdr.dime.glmin = min(double(img(:)));
352 
+
353 
+   if old_RGB & hdr.dime.datatype == 128 & hdr.dime.bitpix == 24
354 
+      img = squeeze(reshape(img, [hdr.dime.dim(2:3) 3 hdr.dime.dim(4) length(img_idx) length(dim5_idx) length(dim6_idx) length(dim7_idx)]));
355 
+      img = permute(img, [1 2 4 3 5 6 7 8]);
356 
+   elseif hdr.dime.datatype == 128 & hdr.dime.bitpix == 24
357 
+      img = squeeze(reshape(img, [3 hdr.dime.dim(2:4) length(img_idx) length(dim5_idx) length(dim6_idx) length(dim7_idx)]));
358 
+      img = permute(img, [2 3 4 1 5 6 7 8]);
359 
+   elseif hdr.dime.datatype == 511 & hdr.dime.bitpix == 96
360 
+      img = double(img);
361 
+      img = (img - min(img))/(max(img) - min(img));
362 
+      img = squeeze(reshape(img, [3 hdr.dime.dim(2:4) length(img_idx) length(dim5_idx) length(dim6_idx) length(dim7_idx)]));
363 
+      img = permute(img, [2 3 4 1 5 6 7 8]);
364 
+   else
365 
+      img = squeeze(reshape(img, [hdr.dime.dim(2:4) length(img_idx) length(dim5_idx) length(dim6_idx) length(dim7_idx)]));
366 
+   end
367 
+
368 
+   if ~isempty(img_idx)
369 
+      hdr.dime.dim(5) = length(img_idx);
370 
+   end
371 
+
372 
+   if ~isempty(dim5_idx)
373 
+      hdr.dime.dim(6) = length(dim5_idx);
374 
+   end
375 
+
376 
+   if ~isempty(dim6_idx)
377 
+      hdr.dime.dim(7) = length(dim6_idx);
378 
+   end
379 
+
380 
+   if ~isempty(dim7_idx)
381 
+      hdr.dime.dim(8) = length(dim7_idx);
382 
+   end
383 
+
384 
+   return						% read_image
385 
+
NIFTI_20090325/load_untouch0_nii_hdr.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,200 @@
1 
+%  internal function
2 
+
3 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
4 
+
5 
+function hdr = load_nii_hdr(fileprefix, machine)
6 
+
7 
+   fn = sprintf('%s.hdr',fileprefix);
8 
+   fid = fopen(fn,'r',machine);
9 
+
10 
+   if fid < 0,
11 
+      msg = sprintf('Cannot open file %s.',fn);
12 
+      error(msg);
13 
+   else
14 
+      fseek(fid,0,'bof');
15 
+      hdr = read_header(fid);
16 
+      fclose(fid);
17 
+   end
18 
+
19 
+   return					% load_nii_hdr
20 
+
21 
+
22 
+%---------------------------------------------------------------------
23 
+function [ dsr ] = read_header(fid)
24 
+
25 
+        %  Original header structures
26 
+	%  struct dsr
27 
+	%       {
28 
+	%       struct header_key hk;            /*   0 +  40       */
29 
+	%       struct image_dimension dime;     /*  40 + 108       */
30 
+	%       struct data_history hist;        /* 148 + 200       */
31 
+	%       };                               /* total= 348 bytes*/
32 
+
33 
+    dsr.hk   = header_key(fid);
34 
+    dsr.dime = image_dimension(fid);
35 
+    dsr.hist = data_history(fid);
36 
+
37 
+    return					% read_header
38 
+
39 
+
40 
+%---------------------------------------------------------------------
41 
+function [ hk ] = header_key(fid)
42 
+
43 
+    fseek(fid,0,'bof');
44 
+
45 
+	%  Original header structures
46 
+	%  struct header_key                     /* header key      */
47 
+	%       {                                /* off + size      */
48 
+	%       int sizeof_hdr                   /*  0 +  4         */
49 
+	%       char data_type[10];              /*  4 + 10         */
50 
+	%       char db_name[18];                /* 14 + 18         */
51 
+	%       int extents;                     /* 32 +  4         */
52 
+	%       short int session_error;         /* 36 +  2         */
53 
+	%       char regular;                    /* 38 +  1         */
54 
+	%       char hkey_un0;                   /* 39 +  1 */
55 
+	%       };                               /* total=40 bytes  */
56 
+	%
57 
+	% int sizeof_header   Should be 348.
58 
+	% char regular        Must be 'r' to indicate that all images and
59 
+	%                     volumes are the same size.
60 
+
61 
+    v6 = version;
62 
+    if str2num(v6(1))<6
63 
+       directchar = '*char';
64 
+    else
65 
+       directchar = 'uchar=>char';
66 
+    end
67 
+
68 
+    hk.sizeof_hdr    = fread(fid, 1,'int32')';	% should be 348!
69 
+    hk.data_type     = deblank(fread(fid,10,directchar)');
70 
+    hk.db_name       = deblank(fread(fid,18,directchar)');
71 
+    hk.extents       = fread(fid, 1,'int32')';
72 
+    hk.session_error = fread(fid, 1,'int16')';
73 
+    hk.regular       = fread(fid, 1,directchar)';
74 
+    hk.hkey_un0      = fread(fid, 1,directchar)';
75 
+
76 
+    return					% header_key
77 
+
78 
+
79 
+%---------------------------------------------------------------------
80 
+function [ dime ] = image_dimension(fid)
81 
+
82 
+	%struct image_dimension
83 
+	%       {                                /* off + size      */
84 
+	%       short int dim[8];                /* 0 + 16          */
85 
+    %           /*
86 
+    %           dim[0]      Number of dimensions in database; usually 4.
87 
+    %           dim[1]      Image X dimension;  number of *pixels* in an image row.
88 
+    %           dim[2]      Image Y dimension;  number of *pixel rows* in slice.
89 
+    %           dim[3]      Volume Z dimension; number of *slices* in a volume.
90 
+    %           dim[4]      Time points; number of volumes in database
91 
+    %           */
92 
+	%       char vox_units[4];               /* 16 + 4          */
93 
+	%       char cal_units[8];               /* 20 + 8          */
94 
+	%       short int unused1;               /* 28 + 2          */
95 
+	%       short int datatype;              /* 30 + 2          */
96 
+	%       short int bitpix;                /* 32 + 2          */
97 
+	%       short int dim_un0;               /* 34 + 2          */
98 
+	%       float pixdim[8];                 /* 36 + 32         */
99 
+	%			/*
100 
+	%				pixdim[] specifies the voxel dimensions:
101 
+	%				pixdim[1] - voxel width, mm
102 
+	%				pixdim[2] - voxel height, mm
103 
+	%				pixdim[3] - slice thickness, mm
104 
+    %               pixdim[4] - volume timing, in msec
105 
+	%					..etc
106 
+	%			*/
107 
+	%       float vox_offset;                /* 68 + 4          */
108 
+	%       float roi_scale;                 /* 72 + 4          */
109 
+	%       float funused1;                  /* 76 + 4          */
110 
+	%       float funused2;                  /* 80 + 4          */
111 
+	%       float cal_max;                   /* 84 + 4          */
112 
+	%       float cal_min;                   /* 88 + 4          */
113 
+	%       int compressed;                  /* 92 + 4          */
114 
+	%       int verified;                    /* 96 + 4          */
115 
+	%       int glmax;                       /* 100 + 4         */
116 
+	%       int glmin;                       /* 104 + 4         */
117 
+	%       };                               /* total=108 bytes */
118 
+
119 
+    v6 = version;
120 
+    if str2num(v6(1))<6
121 
+       directchar = '*char';
122 
+    else
123 
+       directchar = 'uchar=>char';
124 
+    end
125 
+
126 
+    dime.dim        = fread(fid,8,'int16')';
127 
+    dime.vox_units  = deblank(fread(fid,4,directchar)');
128 
+    dime.cal_units  = deblank(fread(fid,8,directchar)');
129 
+    dime.unused1    = fread(fid,1,'int16')';
130 
+    dime.datatype   = fread(fid,1,'int16')';
131 
+    dime.bitpix     = fread(fid,1,'int16')';
132 
+    dime.dim_un0    = fread(fid,1,'int16')';
133 
+    dime.pixdim     = fread(fid,8,'float32')';
134 
+    dime.vox_offset = fread(fid,1,'float32')';
135 
+    dime.roi_scale  = fread(fid,1,'float32')';
136 
+    dime.funused1   = fread(fid,1,'float32')';
137 
+    dime.funused2   = fread(fid,1,'float32')';
138 
+    dime.cal_max    = fread(fid,1,'float32')';
139 
+    dime.cal_min    = fread(fid,1,'float32')';
140 
+    dime.compressed = fread(fid,1,'int32')';
141 
+    dime.verified   = fread(fid,1,'int32')';
142 
+    dime.glmax      = fread(fid,1,'int32')';
143 
+    dime.glmin      = fread(fid,1,'int32')';
144 
+
145 
+    return					% image_dimension
146 
+
147 
+
148 
+%---------------------------------------------------------------------
149 
+function [ hist ] = data_history(fid)
150 
+
151 
+	%struct data_history
152 
+	%       {                                /* off + size      */
153 
+	%       char descrip[80];                /* 0 + 80          */
154 
+	%       char aux_file[24];               /* 80 + 24         */
155 
+	%       char orient;                     /* 104 + 1         */
156 
+	%       char originator[10];             /* 105 + 10        */
157 
+	%       char generated[10];              /* 115 + 10        */
158 
+	%       char scannum[10];                /* 125 + 10        */
159 
+	%       char patient_id[10];             /* 135 + 10        */
160 
+	%       char exp_date[10];               /* 145 + 10        */
161 
+	%       char exp_time[10];               /* 155 + 10        */
162 
+	%       char hist_un0[3];                /* 165 + 3         */
163 
+	%       int views                        /* 168 + 4         */
164 
+	%       int vols_added;                  /* 172 + 4         */
165 
+	%       int start_field;                 /* 176 + 4         */
166 
+	%       int field_skip;                  /* 180 + 4         */
167 
+	%       int omax;                        /* 184 + 4         */
168 
+	%       int omin;                        /* 188 + 4         */
169 
+	%       int smax;                        /* 192 + 4         */
170 
+	%       int smin;                        /* 196 + 4         */
171 
+	%       };                               /* total=200 bytes */
172 
+
173 
+    v6 = version;
174 
+    if str2num(v6(1))<6
175 
+       directchar = '*char';
176 
+    else
177 
+       directchar = 'uchar=>char';
178 
+    end
179 
+
180 
+    hist.descrip     = deblank(fread(fid,80,directchar)');
181 
+    hist.aux_file    = deblank(fread(fid,24,directchar)');
182 
+    hist.orient      = fread(fid, 1,'char')';
183 
+    hist.originator  = fread(fid, 5,'int16')';
184 
+    hist.generated   = deblank(fread(fid,10,directchar)');
185 
+    hist.scannum     = deblank(fread(fid,10,directchar)');
186 
+    hist.patient_id  = deblank(fread(fid,10,directchar)');
187 
+    hist.exp_date    = deblank(fread(fid,10,directchar)');
188 
+    hist.exp_time    = deblank(fread(fid,10,directchar)');
189 
+    hist.hist_un0    = deblank(fread(fid, 3,directchar)');
190 
+    hist.views       = fread(fid, 1,'int32')';
191 
+    hist.vols_added  = fread(fid, 1,'int32')';
192 
+    hist.start_field = fread(fid, 1,'int32')';
193 
+    hist.field_skip  = fread(fid, 1,'int32')';
194 
+    hist.omax        = fread(fid, 1,'int32')';
195 
+    hist.omin        = fread(fid, 1,'int32')';
196 
+    hist.smax        = fread(fid, 1,'int32')';
197 
+    hist.smin        = fread(fid, 1,'int32')';
198 
+
199 
+    return					% data_history
200 
+
NIFTI_20090325/load_untouch_nii.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,106 @@
1 
+%  Load NIFTI or ANALYZE dataset, but not applying any appropriate affine
2 
+%  geometric transform or voxel intensity scaling.
3 
+%
4 
+%  Although according to NIFTI website, all those header information are
5 
+%  supposed to be applied to the loaded NIFTI image, there are some
6 
+%  situations that people do want to leave the original NIFTI header and
7 
+%  data untouched. They will probably just use MATLAB to do certain image
8 
+%  processing regardless of image orientation, and to save data back with
9 
+%  the same NIfTI header.
10 
+%
11 
+%  Since this program is only served for those situations, please use it
12 
+%  together with "save_untouch_nii.m", and do not use "save_nii.m" or
13 
+%  "view_nii.m" for the data that is loaded by "load_untouch_nii.m". For
14 
+%  normal situation, you should use "load_nii.m" instead.
15 
+%
16 
+%  Usage: nii = load_untouch_nii(filename, [img_idx], [dim5_idx], [dim6_idx], [dim7_idx])
17 
+%
18 
+%  filename  - 	NIFTI or ANALYZE file name.
19 
+%
20 
+%  img_idx (optional)  -  a numerical array of image volume indices.
21 
+%	Only the specified volumes will be loaded. All available image
22 
+%	volumes will be loaded, if it is default or empty.
23 
+%
24 
+%	The number of images scans can be obtained from get_nii_frame.m,
25 
+%	or simply: hdr.dime.dim(5).
26 
+%
27 
+%  dim5_idx (optional)  -  a numerical array of 5th dimension indices.
28 
+%	Only the specified range will be loaded. All available range
29 
+%	will be loaded, if it is default or empty.
30 
+%
31 
+%  dim6_idx (optional)  -  a numerical array of 6th dimension indices.
32 
+%	Only the specified range will be loaded. All available range
33 
+%	will be loaded, if it is default or empty.
34 
+%
35 
+%  dim7_idx (optional)  -  a numerical array of 7th dimension indices.
36 
+%	Only the specified range will be loaded. All available range
37 
+%	will be loaded, if it is default or empty.
38 
+%
39 
+%  Returned values:
40 
+%
41 
+%  nii structure:
42 
+%
43 
+%	hdr -		struct with NIFTI header fields.
44 
+%
45 
+%	filetype -	Analyze format .hdr/.img (0);
46 
+%			NIFTI .hdr/.img (1);
47 
+%			NIFTI .nii (2)
48 
+%
49 
+%	fileprefix - 	NIFTI filename without extension.
50 
+%
51 
+%	machine - 	machine string variable.
52 
+%
53 
+%	img - 		3D (or 4D) matrix of NIFTI data.
54 
+%
55 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
56 
+%
57 
+function nii = load_untouch_nii(filename, img_idx, dim5_idx, dim6_idx, dim7_idx)
58 
+
59 
+   if ~exist('filename','var')
60 
+      error('Usage: nii = load_untouch_nii(filename, [img_idx], [dim5_idx], [dim6_idx], [dim7_idx])');
61 
+   end
62 
+
63 
+   if ~exist('img_idx','var') | isempty(img_idx)
64 
+      img_idx = [];
65 
+   end
66 
+
67 
+   if ~exist('dim5_idx','var') | isempty(dim5_idx)
68 
+      dim5_idx = [];
69 
+   end
70 
+
71 
+   if ~exist('dim6_idx','var') | isempty(dim6_idx)
72 
+      dim6_idx = [];
73 
+   end
74 
+
75 
+   if ~exist('dim7_idx','var') | isempty(dim7_idx)
76 
+      dim7_idx = [];
77 
+   end
78 
+
79 
+   %  Read the dataset header
80 
+   %
81 
+   [nii.hdr,nii.filetype,nii.fileprefix,nii.machine] = load_nii_hdr(filename);
82 
+
83 
+   if nii.filetype == 0
84 
+      nii.hdr = load_untouch0_nii_hdr(nii.fileprefix,nii.machine);
85 
+      nii.ext = [];
86 
+   else
87 
+      nii.hdr = load_untouch_nii_hdr(nii.fileprefix,nii.machine,nii.filetype);
88 
+
89 
+      %  Read the header extension
90 
+      %
91 
+      nii.ext = load_nii_ext(filename);
92 
+   end
93 
+
94 
+   %  Read the dataset body
95 
+   %
96 
+   [nii.img,nii.hdr] = load_nii_img(nii.hdr,nii.filetype,nii.fileprefix, ...
97 
+		nii.machine,img_idx,dim5_idx,dim6_idx,dim7_idx);
98 
+
99 
+   %  Perform some of sform/qform transform
100 
+   %
101 
+%   nii = xform_nii(nii, tolerance, preferredForm);
102 
+
103 
+   nii.untouch = 1;
104 
+
105 
+   return					% load_untouch_nii
106 
+
NIFTI_20090325/load_untouch_nii_hdr.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,217 @@
1 
+%  internal function
2 
+
3 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
4 
+
5 
+function hdr = load_nii_hdr(fileprefix, machine, filetype)
6 
+
7 
+   if filetype == 2
8 
+      fn = sprintf('%s.nii',fileprefix);
9 
+
10 
+      if ~exist(fn)
11 
+         msg = sprintf('Cannot find file "%s.nii".', fileprefix);
12 
+         error(msg);
13 
+      end
14 
+   else
15 
+      fn = sprintf('%s.hdr',fileprefix);
16 
+
17 
+      if ~exist(fn)
18 
+         msg = sprintf('Cannot find file "%s.hdr".', fileprefix);
19 
+         error(msg);
20 
+      end
21 
+   end
22 
+
23 
+   fid = fopen(fn,'r',machine);
24 
+
25 
+   if fid < 0,
26 
+      msg = sprintf('Cannot open file %s.',fn);
27 
+      error(msg);
28 
+   else
29 
+      fseek(fid,0,'bof');
30 
+      hdr = read_header(fid);
31 
+      fclose(fid);
32 
+   end
33 
+
34 
+   return					% load_nii_hdr
35 
+
36 
+
37 
+%---------------------------------------------------------------------
38 
+function [ dsr ] = read_header(fid)
39 
+
40 
+        %  Original header structures
41 
+	%  struct dsr
42 
+	%       {
43 
+	%       struct header_key hk;            /*   0 +  40       */
44 
+	%       struct image_dimension dime;     /*  40 + 108       */
45 
+	%       struct data_history hist;        /* 148 + 200       */
46 
+	%       };                               /* total= 348 bytes*/
47 
+
48 
+    dsr.hk   = header_key(fid);
49 
+    dsr.dime = image_dimension(fid);
50 
+    dsr.hist = data_history(fid);
51 
+
52 
+    %  For Analyze data format
53 
+    %
54 
+    if ~strcmp(dsr.hist.magic, 'n+1') & ~strcmp(dsr.hist.magic, 'ni1')
55 
+        dsr.hist.qform_code = 0;
56 
+        dsr.hist.sform_code = 0;
57 
+    end
58 
+
59 
+    return					% read_header
60 
+
61 
+
62 
+%---------------------------------------------------------------------
63 
+function [ hk ] = header_key(fid)
64 
+
65 
+    fseek(fid,0,'bof');
66 
+
67 
+	%  Original header structures
68 
+	%  struct header_key                     /* header key      */
69 
+	%       {                                /* off + size      */
70 
+	%       int sizeof_hdr                   /*  0 +  4         */
71 
+	%       char data_type[10];              /*  4 + 10         */
72 
+	%       char db_name[18];                /* 14 + 18         */
73 
+	%       int extents;                     /* 32 +  4         */
74 
+	%       short int session_error;         /* 36 +  2         */
75 
+	%       char regular;                    /* 38 +  1         */
76 
+	%       char dim_info;   % char hkey_un0;        /* 39 +  1 */
77 
+	%       };                               /* total=40 bytes  */
78 
+	%
79 
+	% int sizeof_header   Should be 348.
80 
+	% char regular        Must be 'r' to indicate that all images and
81 
+	%                     volumes are the same size.
82 
+
83 
+    v6 = version;
84 
+    if str2num(v6(1))<6
85 
+       directchar = '*char';
86 
+    else
87 
+       directchar = 'uchar=>char';
88 
+    end
89 
+
90 
+    hk.sizeof_hdr    = fread(fid, 1,'int32')';	% should be 348!
91 
+    hk.data_type     = deblank(fread(fid,10,directchar)');
92 
+    hk.db_name       = deblank(fread(fid,18,directchar)');
93 
+    hk.extents       = fread(fid, 1,'int32')';
94 
+    hk.session_error = fread(fid, 1,'int16')';
95 
+    hk.regular       = fread(fid, 1,directchar)';
96 
+    hk.dim_info      = fread(fid, 1,'uchar')';
97 
+
98 
+    return					% header_key
99 
+
100 
+
101 
+%---------------------------------------------------------------------
102 
+function [ dime ] = image_dimension(fid)
103 
+
104 
+	%  Original header structures
105 
+	%  struct image_dimension
106 
+	%       {                                /* off + size      */
107 
+	%       short int dim[8];                /* 0 + 16          */
108 
+        %       /*
109 
+        %           dim[0]      Number of dimensions in database; usually 4.
110 
+        %           dim[1]      Image X dimension;  number of *pixels* in an image row.
111 
+        %           dim[2]      Image Y dimension;  number of *pixel rows* in slice.
112 
+        %           dim[3]      Volume Z dimension; number of *slices* in a volume.
113 
+        %           dim[4]      Time points; number of volumes in database
114 
+        %       */
115 
+	%       float intent_p1;   % char vox_units[4];   /* 16 + 4       */
116 
+	%       float intent_p2;   % char cal_units[8];   /* 20 + 4       */
117 
+	%       float intent_p3;   % char cal_units[8];   /* 24 + 4       */
118 
+	%       short int intent_code;   % short int unused1;   /* 28 + 2 */
119 
+	%       short int datatype;              /* 30 + 2          */
120 
+	%       short int bitpix;                /* 32 + 2          */
121 
+	%       short int slice_start;   % short int dim_un0;   /* 34 + 2 */
122 
+	%       float pixdim[8];                 /* 36 + 32         */
123 
+	%	/*
124 
+	%		pixdim[] specifies the voxel dimensions:
125 
+	%		pixdim[1] - voxel width, mm
126 
+	%		pixdim[2] - voxel height, mm
127 
+	%		pixdim[3] - slice thickness, mm
128 
+	%		pixdim[4] - volume timing, in msec
129 
+	%					..etc
130 
+	%	*/
131 
+	%       float vox_offset;                /* 68 + 4          */
132 
+	%       float scl_slope;   % float roi_scale;     /* 72 + 4 */
133 
+	%       float scl_inter;   % float funused1;      /* 76 + 4 */
134 
+	%       short slice_end;   % float funused2;      /* 80 + 2 */
135 
+	%       char slice_code;   % float funused2;      /* 82 + 1 */
136 
+	%       char xyzt_units;   % float funused2;      /* 83 + 1 */
137 
+	%       float cal_max;                   /* 84 + 4          */
138 
+	%       float cal_min;                   /* 88 + 4          */
139 
+	%       float slice_duration;   % int compressed; /* 92 + 4 */
140 
+	%       float toffset;   % int verified;          /* 96 + 4 */
141 
+	%       int glmax;                       /* 100 + 4         */
142 
+	%       int glmin;                       /* 104 + 4         */
143 
+	%       };                               /* total=108 bytes */
144 
+
145 
+    dime.dim        = fread(fid,8,'int16')';
146 
+    dime.intent_p1  = fread(fid,1,'float32')';
147 
+    dime.intent_p2  = fread(fid,1,'float32')';
148 
+    dime.intent_p3  = fread(fid,1,'float32')';
149 
+    dime.intent_code = fread(fid,1,'int16')';
150 
+    dime.datatype   = fread(fid,1,'int16')';
151 
+    dime.bitpix     = fread(fid,1,'int16')';
152 
+    dime.slice_start = fread(fid,1,'int16')';
153 
+    dime.pixdim     = fread(fid,8,'float32')';
154 
+    dime.vox_offset = fread(fid,1,'float32')';
155 
+    dime.scl_slope  = fread(fid,1,'float32')';
156 
+    dime.scl_inter  = fread(fid,1,'float32')';
157 
+    dime.slice_end  = fread(fid,1,'int16')';
158 
+    dime.slice_code = fread(fid,1,'uchar')';
159 
+    dime.xyzt_units = fread(fid,1,'uchar')';
160 
+    dime.cal_max    = fread(fid,1,'float32')';
161 
+    dime.cal_min    = fread(fid,1,'float32')';
162 
+    dime.slice_duration = fread(fid,1,'float32')';
163 
+    dime.toffset    = fread(fid,1,'float32')';
164 
+    dime.glmax      = fread(fid,1,'int32')';
165 
+    dime.glmin      = fread(fid,1,'int32')';
166 
+
167 
+    return					% image_dimension
168 
+
169 
+
170 
+%---------------------------------------------------------------------
171 
+function [ hist ] = data_history(fid)
172 
+
173 
+	%  Original header structures
174 
+	%  struct data_history
175 
+	%       {                                /* off + size      */
176 
+	%       char descrip[80];                /* 0 + 80          */
177 
+	%       char aux_file[24];               /* 80 + 24         */
178 
+	%       short int qform_code;            /* 104 + 2         */
179 
+	%       short int sform_code;            /* 106 + 2         */
180 
+	%       float quatern_b;                 /* 108 + 4         */
181 
+	%       float quatern_c;                 /* 112 + 4         */
182 
+	%       float quatern_d;                 /* 116 + 4         */
183 
+	%       float qoffset_x;                 /* 120 + 4         */
184 
+	%       float qoffset_y;                 /* 124 + 4         */
185 
+	%       float qoffset_z;                 /* 128 + 4         */
186 
+	%       float srow_x[4];                 /* 132 + 16        */
187 
+	%       float srow_y[4];                 /* 148 + 16        */
188 
+	%       float srow_z[4];                 /* 164 + 16        */
189 
+	%       char intent_name[16];            /* 180 + 16        */
190 
+	%       char magic[4];   % int smin;     /* 196 + 4         */
191 
+	%       };                               /* total=200 bytes */
192 
+
193 
+    v6 = version;
194 
+    if str2num(v6(1))<6
195 
+       directchar = '*char';
196 
+    else
197 
+       directchar = 'uchar=>char';
198 
+    end
199 
+
200 
+    hist.descrip     = deblank(fread(fid,80,directchar)');
201 
+    hist.aux_file    = deblank(fread(fid,24,directchar)');
202 
+    hist.qform_code  = fread(fid,1,'int16')';
203 
+    hist.sform_code  = fread(fid,1,'int16')';
204 
+    hist.quatern_b   = fread(fid,1,'float32')';
205 
+    hist.quatern_c   = fread(fid,1,'float32')';
206 
+    hist.quatern_d   = fread(fid,1,'float32')';
207 
+    hist.qoffset_x   = fread(fid,1,'float32')';
208 
+    hist.qoffset_y   = fread(fid,1,'float32')';
209 
+    hist.qoffset_z   = fread(fid,1,'float32')';
210 
+    hist.srow_x      = fread(fid,4,'float32')';
211 
+    hist.srow_y      = fread(fid,4,'float32')';
212 
+    hist.srow_z      = fread(fid,4,'float32')';
213 
+    hist.intent_name = deblank(fread(fid,16,directchar)');
214 
+    hist.magic       = deblank(fread(fid,4,directchar)');
215 
+
216 
+    return					% data_history
217 
+
NIFTI_20090325/make_nii.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,240 @@
1 
+%  Make nii structure specified by an N-D matrix. Usually, N is 3 for
2 
+%  3D matrix [x y z], or 4 for 4D matrix with time series [x y z t].
3 
+%  However, NIfTI allows a maximum of 7D matrix. For RGB24 datatype, an
4 
+%  extra dimension for RGB should be inserted immediately after [x y z].
5 
+%  Optional parameters can also be included, such as: voxel_size,
6 
+%  origin, datatype, and description.
7 
+%
8 
+%  Usage: nii = make_nii(img, [voxel_size], [origin], [datatype], ...
9 
+%		[description])
10 
+%
11 
+%  Where:
12 
+%
13 
+%	img:		Usually, img is a 3D matrix [x y z], or a 4D
14 
+%			matrix with time series [x y z t]. However,
15 
+%			NIfTI allows a maximum of 7D matrix. For RGB
16 
+%			datatype, an extra dimension for RGB should
17 
+%			be inserted immediately after [x y z].
18 
+%
19 
+%	voxel_size (optional):	Voxel size in millimeter for each
20 
+%				dimension. Default is [1 1 1].
21 
+%
22 
+%	origin (optional):	The AC origin. Default is [0 0 0].
23 
+%
24 
+%	datatype (optional):	Storage data type:
25 
+%		2 - uint8,  4 - int16,  8 - int32,  16 - float32,
26 
+%		32 - complex64,  64 - float64,  128 - RGB24,
27 
+%		256 - int8,  512 - uint16,  768 - uint32,
28 
+%		1792 - complex128
29 
+%			Default will use the data type of 'img' matrix
30 
+%
31 
+%	description (optional):	Description of data. Default is ''.
32 
+%
33 
+%  e.g.:
34 
+%     origin = [33 44 13]; datatype = 64;
35 
+%     nii = make_nii(img, [], origin, datatype);    % default voxel_size
36 
+%
37 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
38 
+%
39 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
40 
+%
41 
+function nii = make_nii(varargin)
42 
+
43 
+   nii.img = varargin{1};
44 
+   dims = size(nii.img);
45 
+   dims = [length(dims) dims ones(1,8)];
46 
+   dims = dims(1:8);
47 
+
48 
+   voxel_size = [0 ones(1,7)];
49 
+   origin = zeros(1,5);
50 
+   descrip = '';
51 
+
52 
+   switch class(nii.img)
53 
+      case 'uint8'
54 
+         datatype = 2;
55 
+      case 'int16'
56 
+         datatype = 4;
57 
+      case 'int32'
58 
+         datatype = 8;
59 
+      case 'single'
60 
+         datatype = 16;
61 
+      case 'double'
62 
+         datatype = 64;
63 
+      case 'int8'
64 
+         datatype = 256;
65 
+      case 'uint16'
66 
+         datatype = 512;
67 
+      case 'uint32'
68 
+         datatype = 768;
69 
+      otherwise
70 
+         error('Datatype is not supported by make_nii.');
71 
+   end
72 
+
73 
+   if nargin > 1 & ~isempty(varargin{2})
74 
+      voxel_size(2:4) = double(varargin{2});
75 
+   end
76 
+
77 
+   if nargin > 2 & ~isempty(varargin{3})
78 
+      origin(1:3) = double(varargin{3});
79 
+   end
80 
+
81 
+   if nargin > 3 & ~isempty(varargin{4})
82 
+      datatype = double(varargin{4});
83 
+   end
84 
+
85 
+   if nargin > 4 & ~isempty(varargin{5})
86 
+      descrip = varargin{5};
87 
+   end
88 
+
89 
+   if datatype == 128
90 
+      if ndims(nii.img) > 8
91 
+         error('NIfTI only allows a maximum of 7 Dimension matrix.');
92 
+      end
93 
+
94 
+     dims(1) = dims(1)-1;
95 
+     dims(5:8) = [dims(6:8) 1];
96 
+
97 
+   else
98 
+      if ndims(nii.img) > 7
99 
+         error('NIfTI only allows a maximum of 7 Dimension matrix.');
100 
+      end
101 
+   end
102 
+
103 
+   maxval = round(double(max(nii.img(:))));
104 
+   minval = round(double(min(nii.img(:))));
105 
+
106 
+   nii.hdr = make_header(dims, voxel_size, origin, datatype, ...
107 
+	descrip, maxval, minval);
108 
+
109 
+   switch nii.hdr.dime.datatype
110 
+   case 2
111 
+      nii.img = uint8(nii.img);
112 
+   case 4
113 
+      nii.img = int16(nii.img);
114 
+   case 8
115 
+      nii.img = int32(nii.img);
116 
+   case 16
117 
+      nii.img = single(nii.img);
118 
+   case 32
119 
+      nii.img = single(nii.img);
120 
+   case 64
121 
+      nii.img = double(nii.img);
122 
+   case 128
123 
+      nii.img = uint8(nii.img);
124 
+   case 256
125 
+      nii.img = int8(nii.img);
126 
+   case 512
127 
+      nii.img = uint16(nii.img);
128 
+   case 768
129 
+      nii.img = uint32(nii.img);
130 
+   case 1792
131 
+      nii.img = double(nii.img);
132 
+   otherwise
133 
+      error('Datatype is not supported by make_nii.');
134 
+   end
135 
+
136 
+   return;					% make_nii
137 
+
138 
+
139 
+%---------------------------------------------------------------------
140 
+function hdr = make_header(dims, voxel_size, origin, datatype, ...
141 
+	descrip, maxval, minval)
142 
+
143 
+   hdr.hk   = header_key;
144 
+   hdr.dime = image_dimension(dims, voxel_size, datatype, maxval, minval);
145 
+   hdr.hist = data_history(origin, descrip);
146 
+
147 
+   return;					% make_header
148 
+
149 
+
150 
+%---------------------------------------------------------------------
151 
+function hk = header_key
152 
+
153 
+    hk.sizeof_hdr       = 348;			% must be 348!
154 
+    hk.data_type        = '';
155 
+    hk.db_name          = '';
156 
+    hk.extents          = 0;
157 
+    hk.session_error    = 0;
158 
+    hk.regular          = 'r';
159 
+    hk.dim_info         = 0;
160 
+
161 
+    return;					% header_key
162 
+
163 
+
164 
+%---------------------------------------------------------------------
165 
+function dime = image_dimension(dims, voxel_size, datatype, maxval, minval)
166 
+
167 
+   dime.dim = dims;
168 
+   dime.intent_p1 = 0;
169 
+   dime.intent_p2 = 0;
170 
+   dime.intent_p3 = 0;
171 
+   dime.intent_code = 0;
172 
+   dime.datatype = datatype;
173 
+
174 
+   switch dime.datatype
175 
+   case   2,
176 
+      dime.bitpix = 8;  precision = 'uint8';
177 
+   case   4,
178 
+      dime.bitpix = 16; precision = 'int16';
179 
+   case   8,
180 
+      dime.bitpix = 32; precision = 'int32';
181 
+   case  16,
182 
+      dime.bitpix = 32; precision = 'float32';
183 
+   case  32,
184 
+      dime.bitpix = 64; precision = 'float32';
185 
+   case  64,
186 
+      dime.bitpix = 64; precision = 'float64';
187 
+   case  128,
188 
+      dime.bitpix = 24; precision = 'uint8';
189 
+   case 256
190 
+      dime.bitpix = 8;  precision = 'int8';
191 
+   case 512
192 
+      dime.bitpix = 16; precision = 'uint16';
193 
+   case 768
194 
+      dime.bitpix = 32; precision = 'uint32';
195 
+   case  1792,
196 
+      dime.bitpix = 128; precision = 'float64';
197 
+   otherwise
198 
+      error('Datatype is not supported by make_nii.');
199 
+   end
200 
+
201 
+   dime.slice_start = 0;
202 
+   dime.pixdim = voxel_size;
203 
+   dime.vox_offset = 0;
204 
+   dime.scl_slope = 0;
205 
+   dime.scl_inter = 0;
206 
+   dime.slice_end = 0;
207 
+   dime.slice_code = 0;
208 
+   dime.xyzt_units = 0;
209 
+   dime.cal_max = 0;
210 
+   dime.cal_min = 0;
211 
+   dime.slice_duration = 0;
212 
+   dime.toffset = 0;
213 
+   dime.glmax = maxval;
214 
+   dime.glmin = minval;
215 
+
216 
+   return;					% image_dimension
217 
+
218 
+
219 
+%---------------------------------------------------------------------
220 
+function hist = data_history(origin, descrip)
221 
+
222 
+   hist.descrip = descrip;
223 
+   hist.aux_file = 'none';
224 
+   hist.qform_code = 0;
225 
+   hist.sform_code = 0;
226 
+   hist.quatern_b = 0;
227 
+   hist.quatern_c = 0;
228 
+   hist.quatern_d = 0;
229 
+   hist.qoffset_x = 0;
230 
+   hist.qoffset_y = 0;
231 
+   hist.qoffset_z = 0;
232 
+   hist.srow_x = zeros(1,4);
233 
+   hist.srow_y = zeros(1,4);
234 
+   hist.srow_z = zeros(1,4);
235 
+   hist.intent_name = '';
236 
+   hist.magic = '';
237 
+   hist.originator = origin;
238 
+
239 
+   return;					% data_history
240 
+
NIFTI_20090325/mat_into_hdr.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,83 @@
1 
+%MAT_INTO_HDR  The old versions of SPM (any version before SPM5) store
2 
+%	an affine matrix of the SPM Reoriented image into a matlab file
3 
+%	(.mat extension). The file name of this SPM matlab file is the
4 
+%	same as the SPM Reoriented image file (.img/.hdr extension).
5 
+%
6 
+%	This program will convert the ANALYZE 7.5 SPM Reoriented image
7 
+%	file into NIfTI format, and integrate the affine matrix in the
8 
+%	SPM matlab file into its header file (.hdr extension).
9 
+%
10 
+%	WARNING: Before you run this program, please save the header
11 
+%	file (.hdr extension) into another file name or into another
12 
+%	folder location, because all header files (.hdr extension)
13 
+%	will be overwritten after they are converted into NIfTI
14 
+%	format.
15 
+%
16 
+%  Usage: mat_into_hdr(filename);
17 
+%
18 
+%  filename:	file name(s) with .hdr or .mat file extension, like:
19 
+%		'*.hdr', or '*.mat', or a single .hdr or .mat file.
20 
+%	e.g.	mat_into_hdr('T1.hdr')
21 
+%		mat_into_hdr('*.mat')
22 
+%
23 
+
24 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
25 
+%
26 
+%-------------------------------------------------------------------------
27 
+function mat_into_hdr(files)
28 
+
29 
+   pn = fileparts(files);
30 
+   file_lst = dir(files);
31 
+   file_lst = {file_lst.name};
32 
+   file1 = file_lst{1};
33 
+   [p n e]= fileparts(file1);
34 
+
35 
+   for i=1:length(file_lst)
36 
+      [p n e]= fileparts(file_lst{i});
37 
+      disp(['working on file ', num2str(i) ,' of ', num2str(length(file_lst)), ': ', n,e]);
38 
+      process=1;
39 
+
40 
+      if isequal(e,'.hdr')
41 
+         mat=fullfile(pn, [n,'.mat']);
42 
+         hdr=fullfile(pn, file_lst{i});
43 
+
44 
+         if ~exist(mat,'file')
45 
+            warning(['Cannot find file "',mat  , '". File "', n, e, '" will not be processed.']);
46 
+            process=0;
47 
+         end
48 
+      elseif isequal(e,'.mat')
49 
+         hdr=fullfile(pn, [n,'.hdr']);
50 
+         mat=fullfile(pn, file_lst{i});
51 
+
52 
+         if ~exist(hdr,'file')
53 
+            warning(['Can not find file "',hdr  , '". File "', n, e, '" will not be processed.']);
54 
+            process=0;
55 
+         end
56 
+      else
57 
+         warning(['Input file must have .mat or .hdr extension. File "', n, e, '" will not be processed.']);
58 
+         process=0;
59 
+      end
60 
+
61 
+      if process
62 
+         load(mat);
63 
+         R=M(1:3,1:3);
64 
+         T=M(1:3,4);
65 
+         T=R*ones(3,1)+T;
66 
+         M(1:3,4)=T;
67 
+
68 
+         [h filetype fileprefix machine]=load_nii_hdr(hdr);
69 
+         h.hist.qform_code=0;
70 
+         h.hist.sform_code=1;
71 
+         h.hist.srow_x=M(1,:);
72 
+         h.hist.srow_y=M(2,:);
73 
+         h.hist.srow_z=M(3,:);
74 
+         h.hist.magic='ni1';
75 
+
76 
+         fid = fopen(hdr,'w',machine);
77 
+         save_nii_hdr(h,fid);
78 
+         fclose(fid);
79 
+      end
80 
+   end
81 
+
82 
+   return;				% mat_into_hdr
83 
+
NIFTI_20090325/reslice_nii.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,261 @@
1 
+%  The basic application of the 'reslice_nii.m' program is to perform
2 
+%  any 3D affine transform defined by a NIfTI format image.
3 
+%
4 
+%  In addition, the 'reslice_nii.m' program can also be applied to
5 
+%  generate an isotropic image from either a NIfTI format image or
6 
+%  an ANALYZE format image.
7 
+%
8 
+%  The resliced NIfTI file will always be in RAS orientation.
9 
+%
10 
+%  This program only supports real integer or floating-point data type.
11 
+%  For other data type, the program will exit with an error message
12 
+%  "Transform of this NIFTI data is not supported by the program".
13 
+%
14 
+%  Usage: reslice_nii(old_fn, new_fn, [voxel_size], [verbose], [bg], ...
15 
+%			[method], [img_idx], [preferredForm]);
16 
+%
17 
+%  old_fn  -	filename for original NIfTI file
18 
+%
19 
+%  new_fn  -	filename for resliced NIfTI file
20 
+%
21 
+%  voxel_size (optional)  - size of a voxel in millimeter along x y z
22 
+%		direction for resliced NIfTI file. 'voxel_size' will use
23 
+%		the rounded minimum voxel_size in original NIfTI header,
24 
+%		if it is default or empty.
25 
+%
26 
+%  verbose (optional) - 1, 0
27 
+%			1:  show transforming progress in percentage
28 
+%			2:  progress will not be displayed
29 
+%			'verbose' is 1 if it is default or empty.
30 
+%
31 
+%  bg (optional)  -	background voxel intensity in any extra corner that
32 
+%			is caused by 3D interpolation. 0 in most cases. 'bg'
33 
+%			will be the average of two corner voxel intensities
34 
+%			in original image volume, if it is default or empty.
35 
+%
36 
+%  method (optional)  -	1, 2, or 3
37 
+%			1:  for Trilinear interpolation
38 
+%			2:  for Nearest Neighbor interpolation
39 
+%			3:  for Fischer's Bresenham interpolation
40 
+%			'method' is 1 if it is default or empty.
41 
+%
42 
+%  img_idx (optional)  -  a numerical array of image volume indices. Only
43 
+%		the specified volumes will be loaded. All available image
44 
+%		volumes will be loaded, if it is default or empty.
45 
+%
46 
+%	The number of images scans can be obtained from get_nii_frame.m,
47 
+%	or simply: hdr.dime.dim(5).
48 
+%
49 
+%  preferredForm (optional)  -  selects which transformation from voxels
50 
+%	to RAS coordinates; values are s,q,S,Q.  Lower case s,q indicate
51 
+%	"prefer sform or qform, but use others if preferred not present".
52 
+%	Upper case indicate the program is forced to use the specificied
53 
+%	tranform or fail loading.  'preferredForm' will be 's', if it is
54 
+%	default or empty.	- Jeff Gunter
55 
+%
56 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
57 
+%
58 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
59 
+%
60 
+function reslice_nii(old_fn, new_fn, voxel_size, verbose, bg, method, img_idx, preferredForm)
61 
+
62 
+   if ~exist('old_fn','var') | ~exist('new_fn','var')
63 
+      error('Usage: reslice_nii(old_fn, new_fn, [voxel_size], [verbose], [bg], [method], [img_idx])');
64 
+   end
65 
+
66 
+   if ~exist('method','var') | isempty(method)
67 
+      method = 1;
68 
+   end
69 
+
70 
+   if ~exist('img_idx','var') | isempty(img_idx)
71 
+      img_idx = [];
72 
+   end
73 
+
74 
+   if ~exist('verbose','var') | isempty(verbose)
75 
+      verbose = 1;
76 
+   end
77 
+
78 
+   if ~exist('preferredForm','var') | isempty(preferredForm)
79 
+      preferredForm= 's';				% Jeff
80 
+   end
81 
+
82 
+   nii = load_nii_no_xform(old_fn, img_idx, 0, preferredForm);
83 
+
84 
+   if ~ismember(nii.hdr.dime.datatype, [2,4,8,16,64,256,512,768])
85 
+      error('Transform of this NIFTI data is not supported by the program.');
86 
+   end
87 
+
88 
+   if ~exist('voxel_size','var') | isempty(voxel_size)
89 
+      voxel_size = round(min(nii.hdr.dime.pixdim(2:4)))*ones(1,3);
90 
+   elseif length(voxel_size) < 3
91 
+      voxel_size = voxel_size(1)*ones(1,3);
92 
+   end
93 
+
94 
+   if ~exist('bg','var') | isempty(bg)
95 
+      bg = mean([nii.img(1) nii.img(end)]);
96 
+   end
97 
+
98 
+   old_M = nii.hdr.hist.old_affine;
99 
+
100 
+   if nii.hdr.dime.dim(5) > 1
101 
+      for i = 1:nii.hdr.dime.dim(5)
102 
+         if verbose
103 
+            fprintf('Reslicing %d of %d volumes.\n', i, nii.hdr.dime.dim(5));
104 
+         end
105 
+
106 
+         [img(:,:,:,i) M] = ...
107 
+		affine(nii.img(:,:,:,i), old_M, voxel_size, verbose, bg, method);
108 
+      end
109 
+   else
110 
+      [img M] = affine(nii.img, old_M, voxel_size, verbose, bg, method);
111 
+   end
112 
+
113 
+   new_dim = size(img);
114 
+   nii.img = img;
115 
+   nii.hdr.dime.dim(2:4) = new_dim(1:3);
116 
+   nii.hdr.dime.datatype = 16;
117 
+   nii.hdr.dime.bitpix = 32;
118 
+   nii.hdr.dime.pixdim(2:4) = voxel_size(:)';
119 
+   nii.hdr.dime.glmax = max(img(:));
120 
+   nii.hdr.dime.glmin = min(img(:));
121 
+   nii.hdr.hist.qform_code = 0;
122 
+   nii.hdr.hist.sform_code = 1;
123 
+   nii.hdr.hist.srow_x = M(1,:);
124 
+   nii.hdr.hist.srow_y = M(2,:);
125 
+   nii.hdr.hist.srow_z = M(3,:);
126 
+   nii.hdr.hist.new_affine = M;
127 
+
128 
+   save_nii(nii, new_fn);
129 
+
130 
+   return;					% reslice_nii
131 
+
132 
+
133 
+%--------------------------------------------------------------------
134 
+function [nii] = load_nii_no_xform(filename, img_idx, old_RGB, preferredForm)
135 
+
136 
+   if ~exist('filename','var'),
137 
+      error('Usage: [nii] = load_nii(filename, [img_idx], [old_RGB])');
138 
+   end
139 
+
140 
+   if ~exist('img_idx','var'), img_idx = []; end
141 
+   if ~exist('old_RGB','var'), old_RGB = 0; end
142 
+   if ~exist('preferredForm','var'), preferredForm= 's'; end     % Jeff
143 
+
144 
+   %  Read the dataset header
145 
+   %
146 
+   [nii.hdr,nii.filetype,nii.fileprefix,nii.machine] = load_nii_hdr(filename);
147 
+
148 
+   %  Read the header extension
149 
+   %
150 
+%   nii.ext = load_nii_ext(filename);
151 
+
152 
+   %  Read the dataset body
153 
+   %
154 
+   [nii.img,nii.hdr] = ...
155 
+        load_nii_img(nii.hdr,nii.filetype,nii.fileprefix,nii.machine,img_idx,'','','',old_RGB);
156 
+
157 
+   %  Perform some of sform/qform transform
158 
+   %
159 
+%   nii = xform_nii(nii, preferredForm);
160 
+
161 
+
162 
+   hdr = nii.hdr;
163 
+
164 
+   %  NIFTI can have both sform and qform transform. This program
165 
+   %  will check sform_code prior to qform_code by default.
166 
+   %
167 
+   %  If user specifys "preferredForm", user can then choose the
168 
+   %  priority.					- Jeff
169 
+   %
170 
+   useForm=[];					% Jeff
171 
+
172 
+   if isequal(preferredForm,'S')
173 
+       if isequal(hdr.hist.sform_code,0)
174 
+           error('User requires sform, sform not set in header');
175 
+       else
176 
+           useForm='s';
177 
+       end
178 
+   end						% Jeff
179 
+
180 
+   if isequal(preferredForm,'Q')
181 
+       if isequal(hdr.hist.qform_code,0)
182 
+           error('User requires sform, sform not set in header');
183 
+       else
184 
+           useForm='q';
185 
+       end
186 
+   end						% Jeff
187 
+
188 
+   if isequal(preferredForm,'s')
189 
+       if hdr.hist.sform_code > 0
190 
+           useForm='s';
191 
+       elseif hdr.hist.qform_code > 0
192 
+           useForm='q';
193 
+       end
194 
+   end						% Jeff
195 
+
196 
+   if isequal(preferredForm,'q')
197 
+       if hdr.hist.qform_code > 0
198 
+           useForm='q';
199 
+       elseif hdr.hist.sform_code > 0
200 
+           useForm='s';
201 
+       end
202 
+   end						% Jeff
203 
+
204 
+   if isequal(useForm,'s')
205 
+      R = [hdr.hist.srow_x(1:3)
206 
+           hdr.hist.srow_y(1:3)
207 
+           hdr.hist.srow_z(1:3)];
208 
+
209 
+      T = [hdr.hist.srow_x(4)
210 
+           hdr.hist.srow_y(4)
211 
+           hdr.hist.srow_z(4)];
212 
+
213 
+      nii.hdr.hist.old_affine = [ [R;[0 0 0]] [T;1] ];
214 
+
215 
+   elseif isequal(useForm,'q')
216 
+      b = hdr.hist.quatern_b;
217 
+      c = hdr.hist.quatern_c;
218 
+      d = hdr.hist.quatern_d;
219 
+
220 
+      if 1.0-(b*b+c*c+d*d) < 0
221 
+         if abs(1.0-(b*b+c*c+d*d)) < 1e-5
222 
+            a = 0;
223 
+         else
224 
+            error('Incorrect quaternion values in this NIFTI data.');
225 
+         end
226 
+      else
227 
+         a = sqrt(1.0-(b*b+c*c+d*d));
228 
+      end
229 
+
230 
+      qfac = hdr.dime.pixdim(1);
231 
+      i = hdr.dime.pixdim(2);
232 
+      j = hdr.dime.pixdim(3);
233 
+      k = qfac * hdr.dime.pixdim(4);
234 
+
235 
+      R = [a*a+b*b-c*c-d*d     2*b*c-2*a*d        2*b*d+2*a*c
236 
+           2*b*c+2*a*d         a*a+c*c-b*b-d*d    2*c*d-2*a*b
237 
+           2*b*d-2*a*c         2*c*d+2*a*b        a*a+d*d-c*c-b*b];
238 
+
239 
+      T = [hdr.hist.qoffset_x
240 
+           hdr.hist.qoffset_y
241 
+           hdr.hist.qoffset_z];
242 
+
243 
+      nii.hdr.hist.old_affine = [ [R * diag([i j k]);[0 0 0]] [T;1] ];
244 
+
245 
+   elseif nii.filetype == 0 & exist([nii.fileprefix '.mat'],'file')
246 
+      load([nii.fileprefix '.mat']);	% old SPM affine matrix
247 
+      R=M(1:3,1:3);
248 
+      T=M(1:3,4);
249 
+      T=R*ones(3,1)+T;
250 
+      M(1:3,4)=T;
251 
+      nii.hdr.hist.old_affine = M;
252 
+
253 
+   else
254 
+      M = diag(hdr.dime.pixdim(2:5));
255 
+      M(1:3,4) = -M(1:3,1:3)*(hdr.hist.originator(1:3)-1)';
256 
+      M(4,4) = 1;
257 
+      nii.hdr.hist.old_affine = M;
258 
+   end
259 
+
260 
+   return					% load_nii_no_xform
261 
+
NIFTI_20090325/rri_file_menu.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,179 @@
1 
+%  Imbed a file menu to any figure. If file menu exist, it will append
2 
+%  to the existing file menu. This file menu includes: Copy to clipboard,
3 
+%  print, save, close etc.
4 
+%
5 
+%  Usage: rri_file_menu(fig);
6 
+%
7 
+%         rri_file_menu(fig,0) means no 'Close' menu.
8 
+%
9 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
10 
+%
11 
+%--------------------------------------------------------------------
12 
+
13 
+function rri_file_menu(action, varargin)
14 
+
15 
+   if isnumeric(action)
16 
+      fig = action;
17 
+      action = 'init';
18 
+   end
19 
+
20 
+   %  clear the message line,
21 
+   %
22 
+   h = findobj(gcf,'Tag','MessageLine');
23 
+   set(h,'String','');
24 
+
25 
+   if ~strcmp(action, 'init')
26 
+      set(gcbf, 'InvertHardcopy','off');
27 
+%      set(gcbf, 'PaperPositionMode','auto');
28 
+   end
29 
+
30 
+   switch action
31 
+      case {'init'}
32 
+         if nargin > 1
33 
+            init(fig, 1);		% no 'close' menu
34 
+         else
35 
+            init(fig, 0);
36 
+         end
37 
+      case {'print_fig'}
38 
+         printdlg(gcbf);
39 
+      case {'copy_fig'}
40 
+         copy_fig;
41 
+      case {'export_fig'}
42 
+         export_fig;
43 
+   end
44 
+
45 
+   return					% rri_file_menu
46 
+
47 
+
48 
+%------------------------------------------------
49 
+%
50 
+%  Create (or append) File menu
51 
+%
52 
+function init(fig, no_close)
53 
+
54 
+   %  search for file menu
55 
+   %
56 
+   h_file = [];
57 
+   menuitems = findobj(fig, 'type', 'uimenu');
58 
+
59 
+   for i=1:length(menuitems)
60 
+      filelabel = get(menuitems(i),'label');
61 
+
62 
+      if strcmpi(strrep(filelabel, '&', ''), 'file')
63 
+         h_file = menuitems(i);
64 
+         break;
65 
+      end
66 
+   end
67 
+
68 
+   set(fig, 'menubar', 'none');
69 
+
70 
+   if isempty(h_file)
71 
+      if isempty(menuitems)
72 
+         h_file = uimenu('parent', fig, 'label', 'File');
73 
+      else
74 
+         h_file = uimenu('parent', fig, 'label', 'Copy Figure');
75 
+      end
76 
+
77 
+      h1 = uimenu('parent', h_file, ...
78 
+         'callback','rri_file_menu(''copy_fig'');', ...
79 
+         'label','Copy to Clipboard');
80 
+   else
81 
+      h1 = uimenu('parent', h_file, ...
82 
+         'callback','rri_file_menu(''copy_fig'');', ...
83 
+         'separator','on', ...
84 
+         'label','Copy to Clipboard');
85 
+   end
86 
+
87 
+   h2 = uimenu(h_file, ...
88 
+      'callback','pagesetupdlg(gcbf);', ...
89 
+      'label','Page Setup...');
90 
+
91 
+   h2 = uimenu(h_file, ...
92 
+      'callback','printpreview(gcbf);', ...
93 
+      'label','Print Preview...');
94 
+
95 
+   h2 = uimenu('parent', h_file, ...
96 
+      'callback','printdlg(gcbf);', ...
97 
+      'label','Print Figure ...');
98 
+
99 
+   h2 = uimenu('parent', h_file, ...
100 
+      'callback','rri_file_menu(''export_fig'');', ...
101 
+      'label','Save Figure ...');
102 
+
103 
+   arch = computer;
104 
+   if ~strcmpi(arch(1:2),'PC')
105 
+      set(h1, 'enable', 'off');
106 
+   end
107 
+
108 
+   if ~no_close
109 
+      h1 = uimenu('parent', h_file, ...
110 
+         'callback','close(gcbf);', ...
111 
+         'separator','on', ...
112 
+         'label','Close');
113 
+   end
114 
+
115 
+   return;					% init
116 
+
117 
+
118 
+%------------------------------------------------
119 
+%
120 
+%  Copy to clipboard
121 
+%
122 
+function copy_fig
123 
+
124 
+   arch = computer;
125 
+   if(~strcmpi(arch(1:2),'PC'))
126 
+      error('copy to clipboard can only be used under MS Windows');
127 
+      return;
128 
+   end
129 
+
130 
+   print -noui -dbitmap;
131 
+
132 
+   return					% copy_fig
133 
+
134 
+
135 
+%------------------------------------------------
136 
+%
137 
+%  Save as an image file
138 
+%
139 
+function export_fig
140 
+
141 
+   curr = pwd;
142 
+   if isempty(curr)
143 
+      curr = filesep;
144 
+   end
145 
+
146 
+   [selected_file, selected_path] = rri_select_file(curr,'Save As');
147 
+
148 
+   if isempty(selected_file) | isempty(selected_path)
149 
+      return;
150 
+   end
151 
+
152 
+   filename = [selected_path selected_file];
153 
+
154 
+   if(exist(filename,'file')==2)		% file exist
155 
+
156 
+      dlg_title = 'Confirm File Overwrite';
157 
+      msg = ['File ',filename,' exist. Are you sure you want to overwrite it?'];
158 
+      response = questdlg(msg,dlg_title,'Yes','No','Yes');
159 
+
160 
+      if(strcmp(response,'No'))
161 
+         return;
162 
+      end
163 
+
164 
+   end
165 
+
166 
+   old_pointer = get(gcbf,'pointer');
167 
+   set(gcbf,'pointer','watch');
168 
+
169 
+   try
170 
+      saveas(gcbf,filename);
171 
+   catch
172 
+      msg = 'ERROR: Cannot save file';
173 
+      set(findobj(gcf,'Tag','MessageLine'),'String',msg);
174 
+   end
175 
+
176 
+   set(gcbf,'pointer',old_pointer);
177 
+
178 
+   return;					% export_fig
179 
+
NIFTI_20090325/rri_orient.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,95 @@
1 
+%  Convert image of different orientations to standard Analyze orientation
2 
+%
3 
+%  Usage: nii = rri_orient(nii);
4 
+
5 
+%  Jimmy Shen (jimmy@rotman-baycrest.on.ca), 26-APR-04
6 
+%___________________________________________________________________
7 
+
8 
+function [nii, orient, pattern] = rri_orient(nii, varargin)
9 
+
10 
+   if nargin > 1
11 
+      pattern = varargin{1};
12 
+   else
13 
+      pattern = [];
14 
+   end
15 
+
16 
+   orient = [1 2 3];
17 
+   dim = double(nii.hdr.dime.dim([2:4]));
18 
+
19 
+   if ~isempty(pattern) & ~isequal(length(pattern), prod(dim))
20 
+      return;
21 
+   end
22 
+
23 
+   %  get orient of the current image
24 
+   %
25 
+   orient = rri_orient_ui;
26 
+   pause(.1);
27 
+
28 
+   %  no need for conversion
29 
+   %
30 
+   if isequal(orient, [1 2 3])
31 
+      return;
32 
+   end
33 
+
34 
+   if isempty(pattern)
35 
+      pattern = 1:prod(dim);
36 
+   end
37 
+
38 
+   pattern = reshape(pattern, dim);
39 
+   img = nii.img;
40 
+
41 
+   %  calculate after flip orient
42 
+   %
43 
+   rot_orient = mod(orient + 2, 3) + 1;
44 
+
45 
+   %  do flip:
46 
+   %
47 
+   flip_orient = orient - rot_orient;
48 
+
49 
+   for i = 1:3
50 
+      if flip_orient(i)
51 
+         pattern = flipdim(pattern, i);
52 
+         img = flipdim(img, i);
53 
+      end
54 
+   end
55 
+
56 
+   %  get index of orient (do inverse)
57 
+   %
58 
+   [tmp rot_orient] = sort(rot_orient);
59 
+
60 
+   %  do rotation:
61 
+   %
62 
+   pattern = permute(pattern, rot_orient);
63 
+   img = permute(img, [rot_orient 4 5 6]);
64 
+
65 
+   %  rotate resolution, or 'dim'
66 
+   %
67 
+   new_dim = nii.hdr.dime.dim([2:4]);
68 
+   new_dim = new_dim(rot_orient);
69 
+   nii.hdr.dime.dim([2:4]) = new_dim;
70 
+
71 
+   %  rotate voxel_size, or 'pixdim'
72 
+   %
73 
+   tmp = nii.hdr.dime.pixdim([2:4]);
74 
+   tmp = tmp(rot_orient);
75 
+   nii.hdr.dime.pixdim([2:4]) = tmp;
76 
+
77 
+   %  re-calculate originator
78 
+   %
79 
+   tmp = nii.hdr.hist.originator([1:3]);
80 
+   tmp = tmp(rot_orient);
81 
+   flip_orient = flip_orient(rot_orient);
82 
+
83 
+   for i = 1:3
84 
+      if flip_orient(i) & ~isequal(double(tmp(i)), 0)
85 
+         tmp(i) = int16(double(new_dim(i)) - double(tmp(i)) + 1);
86 
+      end
87 
+   end
88 
+
89 
+   nii.hdr.hist.originator([1:3]) = tmp;
90 
+
91 
+   nii.img = img;
92 
+   pattern = pattern(:);
93 
+
94 
+   return;						% rri_orient
95 
+
NIFTI_20090325/rri_orient_ui.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,251 @@
1 
+%  Return orientation of the current image:
2 
+%	orient is orientation 1x3 matrix, in that:
3 
+%	Three elements represent: [x y z]
4 
+%	Element value:	1 - Left to Right; 2 - Posterior to Anterior;
5 
+%			3 - Inferior to Superior; 4 - Right to Left;
6 
+%			5 - Anterior to Posterior; 6 - Superior to Inferior;
7 
+%  e.g.:
8 
+%	Standard RAS Orientation:	[1 2 3]
9 
+%	Standard RHOS Orientation:	[2 4 3]
10 
+
11 
+%  Jimmy Shen (jimmy@rotman-baycrest.on.ca), 26-APR-04
12 
+%
13 
+function orient = rri_orient_ui(varargin)
14 
+
15 
+   if nargin == 0
16 
+      init;
17 
+      orient_ui_fig = gcf;
18 
+      uiwait;					% wait for user finish
19 
+
20 
+      orient = getappdata(gcf, 'orient');
21 
+
22 
+      if isempty(orient)
23 
+         orient = [1 2 3];
24 
+      end
25 
+
26 
+      if ishandle(orient_ui_fig)
27 
+         close(gcf);
28 
+      end
29 
+
30 
+      return;
31 
+   end
32 
+
33 
+   action = varargin{1};
34 
+
35 
+   if strcmp(action, 'done')
36 
+      click_done;
37 
+   elseif strcmp(action, 'cancel')
38 
+      uiresume;
39 
+   end
40 
+
41 
+   return;						% rri_orient_ui
42 
+
43 
+
44 
+%----------------------------------------------------------------------
45 
+function init
46 
+
47 
+   save_setting_status = 'on';
48 
+   rri_orient_pos = [];
49 
+
50 
+   try
51 
+      load('pls_profile');
52 
+   catch
53 
+   end
54 
+
55 
+   try
56 
+      load('rri_pos_profile');
57 
+   catch
58 
+   end
59 
+
60 
+   if ~isempty(rri_orient_pos) & strcmp(save_setting_status,'on')
61 
+
62 
+      pos = rri_orient_pos;
63 
+
64 
+   else
65 
+
66 
+      w = 0.35;
67 
+      h = 0.4;
68 
+      x = (1-w)/2;
69 
+      y = (1-h)/2;
70 
+
71 
+      pos = [x y w h];
72 
+
73 
+   end
74 
+
75 
+   handles.figure = figure('Color',[0.8 0.8 0.8], ...
76 
+        'Units','normal', ...
77 
+        'Name', 'Convert to standard RAS orientation', ...
78 
+        'NumberTitle','off', ...
79 
+        'MenuBar','none', ...
80 
+        'Position',pos, ...
81 
+        'WindowStyle', 'normal', ...
82 
+        'ToolBar','none');
83 
+
84 
+   h0 = handles.figure;
85 
+   Font.FontUnits  = 'point';
86 
+   Font.FontSize   = 12;
87 
+
88 
+   margin = .1;
89 
+   line_num = 6;
90 
+   line_ht = (1 - margin*2) / line_num;
91 
+
92 
+   x = margin;
93 
+   y = 1 - margin - line_ht;
94 
+   w = 1 - margin * 2;
95 
+   h = line_ht * .7;
96 
+
97 
+   pos = [x y w h];
98 
+
99 
+   handles.Ttit = uicontrol('parent', h0, ...
100 
+	'style','text', ...
101 
+	'unit', 'normal', ...
102 
+	Font, ...
103 
+	'Position',pos, ...
104 
+	'HorizontalAlignment','left',...
105 
+	'background', [0.8 0.8 0.8], ...
106 
+	'string', 'Please input orientation of the current image:');
107 
+
108 
+   y = y - line_ht;
109 
+   w = .2;
110 
+
111 
+   pos = [x y w h];
112 
+
113 
+   handles.Tx_orient = uicontrol('parent', h0, ...
114 
+	'style','text', ...
115 
+	'unit', 'normal', ...
116 
+	Font, ...
117 
+	'Position',pos, ...
118 
+	'HorizontalAlignment','left',...
119 
+	'background', [0.8 0.8 0.8], ...
120 
+	'string', 'X   Axes:');
121 
+
122 
+   y = y - line_ht;
123 
+
124 
+   pos = [x y w h];
125 
+
126 
+   handles.Ty_orient = uicontrol('parent', h0, ...
127 
+	'style','text', ...
128 
+	'unit', 'normal', ...
129 
+	Font, ...
130 
+	'Position',pos, ...
131 
+	'HorizontalAlignment','left',...
132 
+	'background', [0.8 0.8 0.8], ...
133 
+	'string', 'Y   Axes:');
134 
+
135 
+   y = y - line_ht;
136 
+
137 
+   pos = [x y w h];
138 
+
139 
+   handles.Tz_orient = uicontrol('parent', h0, ...
140 
+	'style','text', ...
141 
+	'unit', 'normal', ...
142 
+	Font, ...
143 
+	'Position',pos, ...
144 
+	'HorizontalAlignment','left',...
145 
+	'background', [0.8 0.8 0.8], ...
146 
+	'string', 'Z   Axes:');
147 
+
148 
+   choice = {	'From Left to Right', 'From Posterior to Anterior', ...
149 
+		'From Inferior to Superior', 'From Right to Left', ...
150 
+		'From Anterior to Posterior', 'From Superior to Inferior'	};
151 
+
152 
+   y = 1 - margin - line_ht;
153 
+   y = y - line_ht;
154 
+   w = 1 - margin - x - w;
155 
+   x = 1 - margin - w;
156 
+
157 
+   pos = [x y w h];
158 
+
159 
+   handles.x_orient = uicontrol('parent', h0, ...
160 
+	'style','popupmenu', ...
161 
+	'unit', 'normal', ...
162 
+	Font, ...
163 
+	'Position',pos, ...
164 
+	'HorizontalAlignment','left',...
165 
+	'string', choice, ...
166 
+	'value', 1, ...
167 
+	'background', [1 1 1]);
168 
+
169 
+   y = y - line_ht;
170 
+
171 
+   pos = [x y w h];
172 
+
173 
+   handles.y_orient = uicontrol('parent', h0, ...
174 
+	'style','popupmenu', ...
175 
+	'unit', 'normal', ...
176 
+	Font, ...
177 
+	'Position',pos, ...
178 
+	'HorizontalAlignment','left',...
179 
+	'string', choice, ...
180 
+	'value', 2, ...
181 
+	'background', [1 1 1]);
182 
+
183 
+   y = y - line_ht;
184 
+
185 
+   pos = [x y w h];
186 
+
187 
+   handles.z_orient = uicontrol('parent', h0, ...
188 
+	'style','popupmenu', ...
189 
+	'unit', 'normal', ...
190 
+	Font, ...
191 
+	'Position',pos, ...
192 
+	'HorizontalAlignment','left',...
193 
+	'string', choice, ...
194 
+	'value', 3, ...
195 
+	'background', [1 1 1]);
196 
+
197 
+   x = margin;
198 
+   y = y - line_ht * 1.5;
199 
+   w = .3;
200 
+
201 
+   pos = [x y w h];
202 
+
203 
+   handles.done = uicontrol('parent', h0, ...
204 
+	'unit', 'normal', ...
205 
+	Font, ...
206 
+	'Position',pos, ...
207 
+	'HorizontalAlignment','center',...
208 
+        'callback', 'rri_orient_ui(''done'');', ...
209 
+	'string', 'Done');
210 
+
211 
+   x = 1 - margin - w;
212 
+
213 
+   pos = [x y w h];
214 
+
215 
+   handles.cancel = uicontrol('parent', h0, ...
216 
+	'unit', 'normal', ...
217 
+	Font, ...
218 
+	'Position',pos, ...
219 
+	'HorizontalAlignment','center',...
220 
+        'callback', 'rri_orient_ui(''cancel'');', ...
221 
+	'string', 'Cancel');
222 
+
223 
+   setappdata(h0, 'handles', handles);
224 
+   setappdata(h0, 'orient', [1 2 3]);
225 
+
226 
+   return;						% init
227 
+
228 
+
229 
+%----------------------------------------------------------------------
230 
+function click_done
231 
+
232 
+   handles = getappdata(gcf, 'handles');
233 
+
234 
+   x_orient = get(handles.x_orient, 'value');
235 
+   y_orient = get(handles.y_orient, 'value');
236 
+   z_orient = get(handles.z_orient, 'value');
237 
+
238 
+   orient = [x_orient y_orient z_orient];
239 
+   test_orient = [orient, orient + 3];
240 
+   test_orient = mod(test_orient, 3);
241 
+
242 
+   if length(unique(test_orient)) ~= 3
243 
+      msgbox('Please don''t choose same or opposite direction','Error','modal');
244 
+      return;
245 
+   end
246 
+
247 
+   setappdata(gcf, 'orient', [x_orient y_orient z_orient]);
248 
+   uiresume;
249 
+
250 
+   return;						% click_done
251 
+
NIFTI_20090325/rri_xhair.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,92 @@
1 
+%   rri_xhair: create a pair of full_cross_hair at point [x y] in
2 
+%              axes h_ax, and return xhair struct
3 
+%
4 
+%   Usage: xhair = rri_xhair([x y], xhair, h_ax);
5 
+%
6 
+%   If omit xhair, rri_xhair will create a pair of xhair; otherwise,
7 
+%   rri_xhair will update the xhair. If omit h_ax, current axes will
8 
+%   be used.
9 
+%
10 
+
11 
+%   24-nov-2003 jimmy (jimmy@rotman-baycrest.on.ca)
12 
+%
13 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
14 
+
15 
+function xhair = rri_xhair(varargin)
16 
+
17 
+   if nargin == 0
18 
+      error('Please enter a point position as first argument');
19 
+      return;
20 
+   end
21 
+
22 
+   if nargin > 0
23 
+      p = varargin{1};
24 
+
25 
+      if ~isnumeric(p) | length(p) ~= 2
26 
+         error('Invalid point position');
27 
+         return;
28 
+      else
29 
+         xhair = [];
30 
+      end
31 
+   end
32 
+
33 
+   if nargin > 1
34 
+      xhair = varargin{2};
35 
+
36 
+      if ~isempty(xhair)
37 
+         if ~isstruct(xhair)
38 
+            error('Invalid xhair struct');
39 
+            return;
40 
+         elseif ~isfield(xhair,'lx') | ~isfield(xhair,'ly')
41 
+            error('Invalid xhair struct');
42 
+            return;
43 
+         elseif ~ishandle(xhair.lx) | ~ishandle(xhair.ly)
44 
+            error('Invalid xhair struct');
45 
+            return;
46 
+         end
47 
+
48 
+         lx = xhair.lx;
49 
+         ly = xhair.ly;
50 
+      else
51 
+         lx = [];
52 
+         ly = [];
53 
+      end
54 
+   end
55 
+
56 
+   if nargin > 2
57 
+      h_ax = varargin{3};
58 
+
59 
+      if ~ishandle(h_ax)
60 
+         error('Invalid axes handle');
61 
+         return;
62 
+      elseif ~strcmp(lower(get(h_ax,'type')), 'axes')
63 
+         error('Invalid axes handle');
64 
+         return;
65 
+      end
66 
+   else
67 
+      h_ax = gca;
68 
+   end
69 
+
70 
+   x_range = get(h_ax,'xlim');
71 
+   y_range = get(h_ax,'ylim');
72 
+
73 
+   if ~isempty(xhair)
74 
+      set(lx, 'ydata', [p(2) p(2)]);
75 
+      set(ly, 'xdata', [p(1) p(1)]);
76 
+      set(h_ax, 'selected', 'on');
77 
+      set(h_ax, 'selected', 'off');
78 
+   else
79 
+      figure(get(h_ax,'parent'));
80 
+      axes(h_ax);
81 
+
82 
+      xhair.lx = line('xdata', x_range, 'ydata', [p(2) p(2)], ...
83 
+	'zdata', [11 11], 'color', [1 0 0], 'hittest', 'off');
84 
+      xhair.ly = line('xdata', [p(1) p(1)], 'ydata', y_range, ...
85 
+	'zdata', [11 11], 'color', [1 0 0], 'hittest', 'off');
86 
+   end
87 
+
88 
+   set(h_ax,'xlim',x_range);
89 
+   set(h_ax,'ylim',y_range);
90 
+
91 
+   return;
92 
+
NIFTI_20090325/rri_zoom_menu.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,33 @@
1 
+%  Imbed a zoom menu to any figure.
2 
+%
3 
+%  Usage: rri_zoom_menu(fig);
4 
+%
5 
+
6 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
7 
+%
8 
+%--------------------------------------------------------------------
9 
+function menu_hdl = rri_zoom_menu(fig)
10 
+
11 
+   if isnumeric(fig)
12 
+      menu_hdl = uimenu('Parent',fig, ...
13 
+   	   'Label','Zoom on', ...
14 
+	   'Userdata', 1, ...
15 
+           'Callback','rri_zoom_menu(''zoom'');');
16 
+
17 
+      return;
18 
+   end
19 
+
20 
+   zoom_on_state = get(gcbo,'Userdata');
21 
+
22 
+   if (zoom_on_state == 1)
23 
+      zoom on;
24 
+      set(gcbo,'Userdata',0,'Label','Zoom off');
25 
+      set(gcbf,'pointer','crosshair');
26 
+   else
27 
+      zoom off;
28 
+      set(gcbo,'Userdata',1,'Label','Zoom on');
29 
+      set(gcbf,'pointer','arrow');
30 
+   end
31 
+
32 
+   return					% rri_zoom_menu
33 
+
NIFTI_20090325/save_nii.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,233 @@
1 
+%  Save NIFTI dataset. Support both *.nii and *.hdr/*.img file extension.
2 
+%  If file extension is not provided, *.hdr/*.img will be used as default.
3 
+%
4 
+%  Usage: save_nii(nii, filename, [old_RGB])
5 
+%
6 
+%  nii.hdr - struct with NIFTI header fields (from load_nii.m or make_nii.m)
7 
+%
8 
+%  nii.img - 3D (or 4D) matrix of NIFTI data.
9 
+%
10 
+%  filename - NIFTI file name.
11 
+%
12 
+%  old_RGB    - an optional boolean variable to handle special RGB data
13 
+%       sequence [R1 R2 ... G1 G2 ... B1 B2 ...] that is used only by
14 
+%       AnalyzeDirect (Analyze Software). Since both NIfTI and Analyze
15 
+%       file format use RGB triple [R1 G1 B1 R2 G2 B2 ...] sequentially
16 
+%       for each voxel, this variable is set to FALSE by default. If you
17 
+%       would like the saved image only to be opened by AnalyzeDirect
18 
+%       Software, set old_RGB to TRUE (or 1). It will be set to 0, if it
19 
+%       is default or empty.
20 
+%
21 
+%  Tip: to change the data type, set nii.hdr.dime.datatype,
22 
+%	and nii.hdr.dime.bitpix to:
23 
+%
24 
+%     0 None                     (Unknown bit per voxel) % DT_NONE, DT_UNKNOWN
25 
+%     1 Binary                         (ubit1, bitpix=1) % DT_BINARY
26 
+%     2 Unsigned char         (uchar or uint8, bitpix=8) % DT_UINT8, NIFTI_TYPE_UINT8
27 
+%     4 Signed short                  (int16, bitpix=16) % DT_INT16, NIFTI_TYPE_INT16
28 
+%     8 Signed integer                (int32, bitpix=32) % DT_INT32, NIFTI_TYPE_INT32
29 
+%    16 Floating point    (single or float32, bitpix=32) % DT_FLOAT32, NIFTI_TYPE_FLOAT32
30 
+%    32 Complex, 2 float32      (Use float32, bitpix=64) % DT_COMPLEX64, NIFTI_TYPE_COMPLEX64
31 
+%    64 Double precision  (double or float64, bitpix=64) % DT_FLOAT64, NIFTI_TYPE_FLOAT64
32 
+%   128 Red-Green-Blue            (Use uint8, bitpix=24) % DT_RGB24, NIFTI_TYPE_RGB24
33 
+%   256 Signed char            (schar or int8, bitpix=8) % DT_INT8, NIFTI_TYPE_INT8
34 
+%   512 Unsigned short               (uint16, bitpix=16) % DT_UNINT16, NIFTI_TYPE_UNINT16
35 
+%   768 Unsigned integer             (uint32, bitpix=32) % DT_UNINT32, NIFTI_TYPE_UNINT32
36 
+%  1024 Signed long long              (int64, bitpix=64) % DT_INT64, NIFTI_TYPE_INT64
37 
+%  1280 Unsigned long long           (uint64, bitpix=64) % DT_UINT64, NIFTI_TYPE_UINT64
38 
+%  1536 Long double, float128  (Unsupported, bitpix=128) % DT_FLOAT128, NIFTI_TYPE_FLOAT128
39 
+%  1792 Complex128, 2 float64  (Use float64, bitpix=128) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128
40 
+%  2048 Complex256, 2 float128 (Unsupported, bitpix=256) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128
41 
+%
42 
+%  Part of this file is copied and modified under GNU license from
43 
+%  MRI_TOOLBOX developed by CNSP in Flinders University, Australia
44 
+%
45 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
46 
+%
47 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
48 
+%  - "old_RGB" related codes in "save_nii.m" are added by Mike Harms (2006.06.28)
49 
+%
50 
+function save_nii(nii, fileprefix, old_RGB)
51 
+
52 
+   if ~exist('nii','var') | isempty(nii) | ~isfield(nii,'hdr') | ...
53 
+	~isfield(nii,'img') | ~exist('fileprefix','var') | isempty(fileprefix)
54 
+
55 
+      error('Usage: save_nii(nii, filename, [old_RGB])');
56 
+   end
57 
+
58 
+   if isfield(nii,'untouch') & nii.untouch == 1
59 
+      error('Usage: please use ''save_untouch_nii.m'' for the untouched structure.');
60 
+   end
61 
+
62 
+   if ~exist('old_RGB','var') | isempty(old_RGB)
63 
+      old_RGB = 0;
64 
+   end
65 
+
66 
+   filetype = 1;
67 
+
68 
+   %  Note: fileprefix is actually the filename you want to save
69 
+   %
70 
+   if findstr('.nii',fileprefix)
71 
+      filetype = 2;
72 
+      fileprefix = strrep(fileprefix,'.nii','');
73 
+   end
74 
+
75 
+   if findstr('.hdr',fileprefix)
76 
+      fileprefix = strrep(fileprefix,'.hdr','');
77 
+   end
78 
+
79 
+   if findstr('.img',fileprefix)
80 
+      fileprefix = strrep(fileprefix,'.img','');
81 
+   end
82 
+
83 
+   write_nii(nii, filetype, fileprefix, old_RGB);
84 
+
85 
+   if filetype == 1
86 
+
87 
+      %  So earlier versions of SPM can also open it with correct originator
88 
+      %
89 
+      M=[[diag(nii.hdr.dime.pixdim(2:4)) -[nii.hdr.hist.originator(1:3).*nii.hdr.dime.pixdim(2:4)]'];[0 0 0 1]];
90 
+      save(fileprefix, 'M');
91 
+   end
92 
+
93 
+   return					% save_nii
94 
+
95 
+
96 
+%-----------------------------------------------------------------------------------
97 
+function write_nii(nii, filetype, fileprefix, old_RGB)
98 
+
99 
+   hdr = nii.hdr;
100 
+
101 
+   if isfield(nii,'ext') & ~isempty(nii.ext)
102 
+      ext = nii.ext;
103 
+      [ext, esize_total] = verify_nii_ext(ext);
104 
+   else
105 
+      ext = [];
106 
+   end
107 
+
108 
+   switch double(hdr.dime.datatype),
109 
+   case   1,
110 
+      hdr.dime.bitpix = int16(1 ); precision = 'ubit1';
111 
+   case   2,
112 
+      hdr.dime.bitpix = int16(8 ); precision = 'uint8';
113 
+   case   4,
114 
+      hdr.dime.bitpix = int16(16); precision = 'int16';
115 
+   case   8,
116 
+      hdr.dime.bitpix = int16(32); precision = 'int32';
117 
+   case  16,
118 
+      hdr.dime.bitpix = int16(32); precision = 'float32';
119 
+   case  32,
120 
+      hdr.dime.bitpix = int16(64); precision = 'float32';
121 
+   case  64,
122 
+      hdr.dime.bitpix = int16(64); precision = 'float64';
123 
+   case 128,
124 
+      hdr.dime.bitpix = int16(24); precision = 'uint8';
125 
+   case 256
126 
+      hdr.dime.bitpix = int16(8 ); precision = 'int8';
127 
+   case 512
128 
+      hdr.dime.bitpix = int16(16); precision = 'uint16';
129 
+   case 768
130 
+      hdr.dime.bitpix = int16(32); precision = 'uint32';
131 
+   case 1024
132 
+      hdr.dime.bitpix = int16(64); precision = 'int64';
133 
+   case 1280
134 
+      hdr.dime.bitpix = int16(64); precision = 'uint64';
135 
+   case 1792,
136 
+      hdr.dime.bitpix = int16(128); precision = 'float64';
137 
+   otherwise
138 
+      error('This datatype is not supported');
139 
+   end
140 
+
141 
+   hdr.dime.glmax = round(double(max(nii.img(:))));
142 
+   hdr.dime.glmin = round(double(min(nii.img(:))));
143 
+
144 
+   if filetype == 2
145 
+      fid = fopen(sprintf('%s.nii',fileprefix),'w');
146 
+
147 
+      if fid < 0,
148 
+         msg = sprintf('Cannot open file %s.nii.',fileprefix);
149 
+         error(msg);
150 
+      end
151 
+
152 
+      hdr.dime.vox_offset = 352;
153 
+
154 
+      if ~isempty(ext)
155 
+         hdr.dime.vox_offset = hdr.dime.vox_offset + esize_total;
156 
+      end
157 
+
158 
+      hdr.hist.magic = 'n+1';
159 
+      save_nii_hdr(hdr, fid);
160 
+
161 
+      if ~isempty(ext)
162 
+         save_nii_ext(ext, fid);
163 
+      end
164 
+   else
165 
+      fid = fopen(sprintf('%s.hdr',fileprefix),'w');
166 
+
167 
+      if fid < 0,
168 
+         msg = sprintf('Cannot open file %s.hdr.',fileprefix);
169 
+         error(msg);
170 
+      end
171 
+
172 
+      hdr.dime.vox_offset = 0;
173 
+      hdr.hist.magic = 'ni1';
174 
+      save_nii_hdr(hdr, fid);
175 
+
176 
+      if ~isempty(ext)
177 
+         save_nii_ext(ext, fid);
178 
+      end
179 
+
180 
+      fclose(fid);
181 
+      fid = fopen(sprintf('%s.img',fileprefix),'w');
182 
+   end
183 
+
184 
+   ScanDim = double(hdr.dime.dim(5));		% t
185 
+   SliceDim = double(hdr.dime.dim(4));		% z
186 
+   RowDim   = double(hdr.dime.dim(3));		% y
187 
+   PixelDim = double(hdr.dime.dim(2));		% x
188 
+   SliceSz  = double(hdr.dime.pixdim(4));
189 
+   RowSz    = double(hdr.dime.pixdim(3));
190 
+   PixelSz  = double(hdr.dime.pixdim(2));
191 
+
192 
+   x = 1:PixelDim;
193 
+
194 
+   if filetype == 2 & isempty(ext)
195 
+      skip_bytes = double(hdr.dime.vox_offset) - 348;
196 
+   else
197 
+      skip_bytes = 0;
198 
+   end
199 
+
200 
+   if double(hdr.dime.datatype) == 128
201 
+
202 
+      %  RGB planes are expected to be in the 4th dimension of nii.img
203 
+      %
204 
+      if(size(nii.img,4)~=3)
205 
+         error(['The NII structure does not appear to have 3 RGB color planes in the 4th dimension']);
206 
+      end
207 
+
208 
+      if old_RGB
209 
+         nii.img = permute(nii.img, [1 2 4 3 5 6 7 8]);
210 
+      else
211 
+         nii.img = permute(nii.img, [4 1 2 3 5 6 7 8]);
212 
+      end
213 
+   end
214 
+
215 
+   %  For complex float32 or complex float64, voxel values
216 
+   %  include [real, imag]
217 
+   %
218 
+   if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
219 
+      real_img = real(nii.img(:))';
220 
+      nii.img = imag(nii.img(:))';
221 
+      nii.img = [real_img; nii.img];
222 
+   end
223 
+
224 
+   if skip_bytes
225 
+      fwrite(fid, ones(1,skip_bytes), 'uint8');
226 
+   end
227 
+
228 
+   fwrite(fid, nii.img, precision);
229 
+%   fwrite(fid, nii.img, precision, skip_bytes);        % error using skip
230 
+   fclose(fid);
231 
+
232 
+   return;					% write_nii
233 
+
NIFTI_20090325/save_nii_ext.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,38 @@
1 
+%  Save NIFTI header extension.
2 
+%
3 
+%  Usage: save_nii_ext(ext, fid)
4 
+%
5 
+%  ext - struct with NIFTI header extension fields.
6 
+%
7 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
8 
+%
9 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
10 
+%
11 
+function save_nii_ext(ext, fid)
12 
+
13 
+   if ~exist('ext','var') | ~exist('fid','var')
14 
+      error('Usage: save_nii_ext(ext, fid)');
15 
+   end
16 
+
17 
+   if ~isfield(ext,'extension') | ~isfield(ext,'section') | ~isfield(ext,'num_ext')
18 
+      error('Wrong header extension');
19 
+   end
20 
+
21 
+   write_ext(ext, fid);
22 
+
23 
+   return;                                      % save_nii_ext
24 
+
25 
+
26 
+%---------------------------------------------------------------------
27 
+function write_ext(ext, fid)
28 
+
29 
+   fwrite(fid, ext.extension, 'uchar');
30 
+
31 
+   for i=1:ext.num_ext
32 
+      fwrite(fid, ext.section(i).esize, 'int32');
33 
+      fwrite(fid, ext.section(i).ecode, 'int32');
34 
+      fwrite(fid, ext.section(i).edata, 'uchar');
35 
+   end
36 
+
37 
+   return;                                      % write_ext
38 
+
NIFTI_20090325/save_nii_hdr.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,239 @@
1 
+%  Save NIFTI dataset header. Support both *.nii and *.hdr/*.img file
2 
+%  extension.
3 
+%
4 
+%  Usage: save_nii_hdr(hdr, fid)
5 
+%
6 
+%  hdr - struct with NIFTI header fields.
7 
+%
8 
+%  fileprefix - NIFTI file name without extension.
9 
+%
10 
+%  Part of this file is copied and modified under GNU license from
11 
+%  MRI_TOOLBOX developed by CNSP in Flinders University, Australia
12 
+%
13 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
14 
+%
15 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
16 
+%
17 
+function save_nii_hdr(hdr, fid)
18 
+
19 
+   if ~exist('hdr','var') | ~exist('fid','var')
20 
+      error('Usage: save_nii_hdr(hdr, fid)');
21 
+   end
22 
+
23 
+   if ~isequal(hdr.hk.sizeof_hdr,348),
24 
+      error('hdr.hk.sizeof_hdr must be 348.');
25 
+   end
26 
+
27 
+   if hdr.hist.qform_code == 0 & hdr.hist.sform_code == 0
28 
+      hdr.hist.sform_code = 1;
29 
+      hdr.hist.srow_x(1) = hdr.dime.pixdim(2);
30 
+      hdr.hist.srow_x(2) = 0;
31 
+      hdr.hist.srow_x(3) = 0;
32 
+      hdr.hist.srow_y(1) = 0;
33 
+      hdr.hist.srow_y(2) = hdr.dime.pixdim(3);
34 
+      hdr.hist.srow_y(3) = 0;
35 
+      hdr.hist.srow_z(1) = 0;
36 
+      hdr.hist.srow_z(2) = 0;
37 
+      hdr.hist.srow_z(3) = hdr.dime.pixdim(4);
38 
+      hdr.hist.srow_x(4) = (1-hdr.hist.originator(1))*hdr.dime.pixdim(2);
39 
+      hdr.hist.srow_y(4) = (1-hdr.hist.originator(2))*hdr.dime.pixdim(3);
40 
+      hdr.hist.srow_z(4) = (1-hdr.hist.originator(3))*hdr.dime.pixdim(4);
41 
+   end
42 
+
43 
+   write_header(hdr, fid);
44 
+
45 
+   return;					% save_nii_hdr
46 
+
47 
+
48 
+%---------------------------------------------------------------------
49 
+function write_header(hdr, fid)
50 
+
51 
+        %  Original header structures
52 
+	%  struct dsr				/* dsr = hdr */
53 
+	%       {
54 
+	%       struct header_key hk;            /*   0 +  40       */
55 
+	%       struct image_dimension dime;     /*  40 + 108       */
56 
+	%       struct data_history hist;        /* 148 + 200       */
57 
+	%       };                               /* total= 348 bytes*/
58 
+
59 
+   header_key(fid, hdr.hk);
60 
+   image_dimension(fid, hdr.dime);
61 
+   data_history(fid, hdr.hist);
62 
+
63 
+   %  check the file size is 348 bytes
64 
+   %
65 
+   fbytes = ftell(fid);
66 
+
67 
+   if ~isequal(fbytes,348),
68 
+      msg = sprintf('Header size is not 348 bytes.');
69 
+      warning(msg);
70 
+   end
71 
+
72 
+   return;					% write_header
73 
+
74 
+
75 
+%---------------------------------------------------------------------
76 
+function header_key(fid, hk)
77 
+
78 
+   fseek(fid,0,'bof');
79 
+
80 
+	%  Original header structures
81 
+	%  struct header_key                      /* header key      */
82 
+	%       {                                /* off + size      */
83 
+	%       int sizeof_hdr                   /*  0 +  4         */
84 
+	%       char data_type[10];              /*  4 + 10         */
85 
+	%       char db_name[18];                /* 14 + 18         */
86 
+	%       int extents;                     /* 32 +  4         */
87 
+	%       short int session_error;         /* 36 +  2         */
88 
+	%       char regular;                    /* 38 +  1         */
89 
+	%       char dim_info;   % char hkey_un0;        /* 39 +  1 */
90 
+	%       };                               /* total=40 bytes  */
91 
+
92 
+   fwrite(fid, hk.sizeof_hdr(1),    'int32');	% must be 348.
93 
+
94 
+   % data_type = sprintf('%-10s',hk.data_type);	% ensure it is 10 chars from left
95 
+   % fwrite(fid, data_type(1:10), 'uchar');
96 
+   pad = zeros(1, 10-length(hk.data_type));
97 
+   hk.data_type = [hk.data_type  char(pad)];
98 
+   fwrite(fid, hk.data_type(1:10), 'uchar');
99 
+
100 
+   % db_name   = sprintf('%-18s', hk.db_name);	% ensure it is 18 chars from left
101 
+   % fwrite(fid, db_name(1:18), 'uchar');
102 
+   pad = zeros(1, 18-length(hk.db_name));
103 
+   hk.db_name = [hk.db_name  char(pad)];
104 
+   fwrite(fid, hk.db_name(1:18), 'uchar');
105 
+
106 
+   fwrite(fid, hk.extents(1),       'int32');
107 
+   fwrite(fid, hk.session_error(1), 'int16');
108 
+   fwrite(fid, hk.regular(1),       'uchar');	% might be uint8
109 
+
110 
+   % fwrite(fid, hk.hkey_un0(1),    'uchar');
111 
+   % fwrite(fid, hk.hkey_un0(1),    'uint8');
112 
+   fwrite(fid, hk.dim_info(1),      'uchar');
113 
+
114 
+   return;					% header_key
115 
+
116 
+
117 
+%---------------------------------------------------------------------
118 
+function image_dimension(fid, dime)
119 
+
120 
+	%  Original header structures
121 
+	%  struct image_dimension
122 
+	%       {                                /* off + size      */
123 
+	%       short int dim[8];                /* 0 + 16          */
124 
+	%       float intent_p1;   % char vox_units[4];   /* 16 + 4       */
125 
+	%       float intent_p2;   % char cal_units[8];   /* 20 + 4       */
126 
+	%       float intent_p3;   % char cal_units[8];   /* 24 + 4       */
127 
+	%       short int intent_code;   % short int unused1;   /* 28 + 2 */
128 
+	%       short int datatype;              /* 30 + 2          */
129 
+	%       short int bitpix;                /* 32 + 2          */
130 
+	%       short int slice_start;   % short int dim_un0;   /* 34 + 2 */
131 
+	%       float pixdim[8];                 /* 36 + 32         */
132 
+	%			/*
133 
+	%				pixdim[] specifies the voxel dimensions:
134 
+	%				pixdim[1] - voxel width
135 
+	%				pixdim[2] - voxel height
136 
+	%				pixdim[3] - interslice distance
137 
+	%				pixdim[4] - volume timing, in msec
138 
+	%					..etc
139 
+	%			*/
140 
+	%       float vox_offset;                /* 68 + 4          */
141 
+	%       float scl_slope;   % float roi_scale;     /* 72 + 4 */
142 
+	%       float scl_inter;   % float funused1;      /* 76 + 4 */
143 
+	%       short slice_end;   % float funused2;      /* 80 + 2 */
144 
+	%       char slice_code;   % float funused2;      /* 82 + 1 */
145 
+	%       char xyzt_units;   % float funused2;      /* 83 + 1 */
146 
+	%       float cal_max;                   /* 84 + 4          */
147 
+	%       float cal_min;                   /* 88 + 4          */
148 
+	%       float slice_duration;   % int compressed; /* 92 + 4 */
149 
+	%       float toffset;   % int verified;          /* 96 + 4 */
150 
+	%       int glmax;                       /* 100 + 4         */
151 
+	%       int glmin;                       /* 104 + 4         */
152 
+	%       };                               /* total=108 bytes */
153 
+
154 
+   fwrite(fid, dime.dim(1:8),        'int16');
155 
+   fwrite(fid, dime.intent_p1(1),  'float32');
156 
+   fwrite(fid, dime.intent_p2(1),  'float32');
157 
+   fwrite(fid, dime.intent_p3(1),  'float32');
158 
+   fwrite(fid, dime.intent_code(1),  'int16');
159 
+   fwrite(fid, dime.datatype(1),     'int16');
160 
+   fwrite(fid, dime.bitpix(1),       'int16');
161 
+   fwrite(fid, dime.slice_start(1),  'int16');
162 
+   fwrite(fid, dime.pixdim(1:8),   'float32');
163 
+   fwrite(fid, dime.vox_offset(1), 'float32');
164 
+   fwrite(fid, dime.scl_slope(1),  'float32');
165 
+   fwrite(fid, dime.scl_inter(1),  'float32');
166 
+   fwrite(fid, dime.slice_end(1),    'int16');
167 
+   fwrite(fid, dime.slice_code(1),   'uchar');
168 
+   fwrite(fid, dime.xyzt_units(1),   'uchar');
169 
+   fwrite(fid, dime.cal_max(1),    'float32');
170 
+   fwrite(fid, dime.cal_min(1),    'float32');
171 
+   fwrite(fid, dime.slice_duration(1), 'float32');
172 
+   fwrite(fid, dime.toffset(1),    'float32');
173 
+   fwrite(fid, dime.glmax(1),        'int32');
174 
+   fwrite(fid, dime.glmin(1),        'int32');
175 
+
176 
+   return;					% image_dimension
177 
+
178 
+
179 
+%---------------------------------------------------------------------
180 
+function data_history(fid, hist)
181 
+
182 
+	% Original header structures
183 
+	%struct data_history
184 
+	%       {                                /* off + size      */
185 
+	%       char descrip[80];                /* 0 + 80          */
186 
+	%       char aux_file[24];               /* 80 + 24         */
187 
+	%       short int qform_code;            /* 104 + 2         */
188 
+	%       short int sform_code;            /* 106 + 2         */
189 
+	%       float quatern_b;                 /* 108 + 4         */
190 
+	%       float quatern_c;                 /* 112 + 4         */
191 
+	%       float quatern_d;                 /* 116 + 4         */
192 
+	%       float qoffset_x;                 /* 120 + 4         */
193 
+	%       float qoffset_y;                 /* 124 + 4         */
194 
+	%       float qoffset_z;                 /* 128 + 4         */
195 
+	%       float srow_x[4];                 /* 132 + 16        */
196 
+	%       float srow_y[4];                 /* 148 + 16        */
197 
+	%       float srow_z[4];                 /* 164 + 16        */
198 
+	%       char intent_name[16];            /* 180 + 16        */
199 
+	%       char magic[4];   % int smin;     /* 196 + 4         */
200 
+	%       };                               /* total=200 bytes */
201 
+
202 
+   % descrip     = sprintf('%-80s', hist.descrip);     % 80 chars from left
203 
+   % fwrite(fid, descrip(1:80),    'uchar');
204 
+   pad = zeros(1, 80-length(hist.descrip));
205 
+   hist.descrip = [hist.descrip  char(pad)];
206 
+   fwrite(fid, hist.descrip(1:80), 'uchar');
207 
+
208 
+   % aux_file    = sprintf('%-24s', hist.aux_file);    % 24 chars from left
209 
+   % fwrite(fid, aux_file(1:24),   'uchar');
210 
+   pad = zeros(1, 24-length(hist.aux_file));
211 
+   hist.aux_file = [hist.aux_file  char(pad)];
212 
+   fwrite(fid, hist.aux_file(1:24), 'uchar');
213 
+
214 
+   fwrite(fid, hist.qform_code,    'int16');
215 
+   fwrite(fid, hist.sform_code,    'int16');
216 
+   fwrite(fid, hist.quatern_b,   'float32');
217 
+   fwrite(fid, hist.quatern_c,   'float32');
218 
+   fwrite(fid, hist.quatern_d,   'float32');
219 
+   fwrite(fid, hist.qoffset_x,   'float32');
220 
+   fwrite(fid, hist.qoffset_y,   'float32');
221 
+   fwrite(fid, hist.qoffset_z,   'float32');
222 
+   fwrite(fid, hist.srow_x(1:4), 'float32');
223 
+   fwrite(fid, hist.srow_y(1:4), 'float32');
224 
+   fwrite(fid, hist.srow_z(1:4), 'float32');
225 
+
226 
+   % intent_name = sprintf('%-16s', hist.intent_name);	% 16 chars from left
227 
+   % fwrite(fid, intent_name(1:16),    'uchar');
228 
+   pad = zeros(1, 16-length(hist.intent_name));
229 
+   hist.intent_name = [hist.intent_name  char(pad)];
230 
+   fwrite(fid, hist.intent_name(1:16), 'uchar');
231 
+
232 
+   % magic	= sprintf('%-4s', hist.magic);		% 4 chars from left
233 
+   % fwrite(fid, magic(1:4),           'uchar');
234 
+   pad = zeros(1, 4-length(hist.magic));
235 
+   hist.magic = [hist.magic  char(pad)];
236 
+   fwrite(fid, hist.magic(1:4),        'uchar');
237 
+
238 
+   return;					% data_history
239 
+
NIFTI_20090325/save_untouch0_nii_hdr.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,219 @@
1 
+%  internal function
2 
+
3 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
4 
+
5 
+function save_nii_hdr(hdr, fid)
6 
+
7 
+   if ~isequal(hdr.hk.sizeof_hdr,348),
8 
+      error('hdr.hk.sizeof_hdr must be 348.');
9 
+   end
10 
+
11 
+   write_header(hdr, fid);
12 
+
13 
+   return;					% save_nii_hdr
14 
+
15 
+
16 
+%---------------------------------------------------------------------
17 
+function write_header(hdr, fid)
18 
+
19 
+        %  Original header structures
20 
+	%  struct dsr				/* dsr = hdr */
21 
+	%       {
22 
+	%       struct header_key hk;            /*   0 +  40       */
23 
+	%       struct image_dimension dime;     /*  40 + 108       */
24 
+	%       struct data_history hist;        /* 148 + 200       */
25 
+	%       };                               /* total= 348 bytes*/
26 
+
27 
+   header_key(fid, hdr.hk);
28 
+   image_dimension(fid, hdr.dime);
29 
+   data_history(fid, hdr.hist);
30 
+
31 
+   %  check the file size is 348 bytes
32 
+   %
33 
+   fbytes = ftell(fid);
34 
+
35 
+   if ~isequal(fbytes,348),
36 
+      msg = sprintf('Header size is not 348 bytes.');
37 
+      warning(msg);
38 
+   end
39 
+
40 
+   return;					% write_header
41 
+
42 
+
43 
+%---------------------------------------------------------------------
44 
+function header_key(fid, hk)
45 
+
46 
+   fseek(fid,0,'bof');
47 
+
48 
+	%  Original header structures
49 
+	%  struct header_key                      /* header key      */
50 
+	%       {                                /* off + size      */
51 
+	%       int sizeof_hdr                   /*  0 +  4         */
52 
+	%       char data_type[10];              /*  4 + 10         */
53 
+	%       char db_name[18];                /* 14 + 18         */
54 
+	%       int extents;                     /* 32 +  4         */
55 
+	%       short int session_error;         /* 36 +  2         */
56 
+	%       char regular;                    /* 38 +  1         */
57 
+	%       char hkey_un0;                   /* 39 +  1 */
58 
+	%       };                               /* total=40 bytes  */
59 
+
60 
+   fwrite(fid, hk.sizeof_hdr(1),    'int32');	% must be 348.
61 
+
62 
+   % data_type = sprintf('%-10s',hk.data_type);	% ensure it is 10 chars from left
63 
+   % fwrite(fid, data_type(1:10), 'uchar');
64 
+   pad = zeros(1, 10-length(hk.data_type));
65 
+   hk.data_type = [hk.data_type  char(pad)];
66 
+   fwrite(fid, hk.data_type(1:10), 'uchar');
67 
+
68 
+   % db_name   = sprintf('%-18s', hk.db_name);	% ensure it is 18 chars from left
69 
+   % fwrite(fid, db_name(1:18), 'uchar');
70 
+   pad = zeros(1, 18-length(hk.db_name));
71 
+   hk.db_name = [hk.db_name  char(pad)];
72 
+   fwrite(fid, hk.db_name(1:18), 'uchar');
73 
+
74 
+   fwrite(fid, hk.extents(1),       'int32');
75 
+   fwrite(fid, hk.session_error(1), 'int16');
76 
+   fwrite(fid, hk.regular(1),       'uchar');
77 
+
78 
+   fwrite(fid, hk.hkey_un0(1),    'uchar');
79 
+
80 
+   return;					% header_key
81 
+
82 
+
83 
+%---------------------------------------------------------------------
84 
+function image_dimension(fid, dime)
85 
+
86 
+	%struct image_dimension
87 
+	%       {                                /* off + size      */
88 
+	%       short int dim[8];                /* 0 + 16          */
89 
+	%       char vox_units[4];               /* 16 + 4          */
90 
+	%       char cal_units[8];               /* 20 + 8          */
91 
+	%       short int unused1;               /* 28 + 2          */
92 
+	%       short int datatype;              /* 30 + 2          */
93 
+	%       short int bitpix;                /* 32 + 2          */
94 
+	%       short int dim_un0;               /* 34 + 2          */
95 
+	%       float pixdim[8];                 /* 36 + 32         */
96 
+	%			/*
97 
+	%				pixdim[] specifies the voxel dimensions:
98 
+	%				pixdim[1] - voxel width
99 
+	%				pixdim[2] - voxel height
100 
+	%				pixdim[3] - interslice distance
101 
+	%					..etc
102 
+	%			*/
103 
+	%       float vox_offset;                /* 68 + 4          */
104 
+	%       float roi_scale;                 /* 72 + 4          */
105 
+	%       float funused1;                  /* 76 + 4          */
106 
+	%       float funused2;                  /* 80 + 4          */
107 
+	%       float cal_max;                   /* 84 + 4          */
108 
+	%       float cal_min;                   /* 88 + 4          */
109 
+	%       int compressed;                  /* 92 + 4          */
110 
+	%       int verified;                    /* 96 + 4          */
111 
+	%       int glmax;                       /* 100 + 4         */
112 
+	%       int glmin;                       /* 104 + 4         */
113 
+	%       };                               /* total=108 bytes */
114 
+
115 
+   fwrite(fid, dime.dim(1:8),      'int16');
116 
+
117 
+   pad = zeros(1, 4-length(dime.vox_units));
118 
+   dime.vox_units = [dime.vox_units  char(pad)];
119 
+   fwrite(fid, dime.vox_units(1:4),  'uchar');
120 
+
121 
+   pad = zeros(1, 8-length(dime.cal_units));
122 
+   dime.cal_units = [dime.cal_units  char(pad)];
123 
+   fwrite(fid, dime.cal_units(1:8),  'uchar');
124 
+
125 
+   fwrite(fid, dime.unused1(1),    'int16');
126 
+   fwrite(fid, dime.datatype(1),   'int16');
127 
+   fwrite(fid, dime.bitpix(1),     'int16');
128 
+   fwrite(fid, dime.dim_un0(1),    'int16');
129 
+   fwrite(fid, dime.pixdim(1:8),   'float32');
130 
+   fwrite(fid, dime.vox_offset(1), 'float32');
131 
+   fwrite(fid, dime.roi_scale(1),  'float32');
132 
+   fwrite(fid, dime.funused1(1),   'float32');
133 
+   fwrite(fid, dime.funused2(1),   'float32');
134 
+   fwrite(fid, dime.cal_max(1),    'float32');
135 
+   fwrite(fid, dime.cal_min(1),    'float32');
136 
+   fwrite(fid, dime.compressed(1), 'int32');
137 
+   fwrite(fid, dime.verified(1),   'int32');
138 
+   fwrite(fid, dime.glmax(1),      'int32');
139 
+   fwrite(fid, dime.glmin(1),      'int32');
140 
+
141 
+   return;					% image_dimension
142 
+
143 
+
144 
+%---------------------------------------------------------------------
145 
+function data_history(fid, hist)
146 
+
147 
+	% Original header structures - ANALYZE 7.5
148 
+	%struct data_history
149 
+	%       {                                /* off + size      */
150 
+	%       char descrip[80];                /* 0 + 80          */
151 
+	%       char aux_file[24];               /* 80 + 24         */
152 
+	%       char orient;                     /* 104 + 1         */
153 
+	%       char originator[10];             /* 105 + 10        */
154 
+	%       char generated[10];              /* 115 + 10        */
155 
+	%       char scannum[10];                /* 125 + 10        */
156 
+	%       char patient_id[10];             /* 135 + 10        */
157 
+	%       char exp_date[10];               /* 145 + 10        */
158 
+	%       char exp_time[10];               /* 155 + 10        */
159 
+	%       char hist_un0[3];                /* 165 + 3         */
160 
+	%       int views                        /* 168 + 4         */
161 
+	%       int vols_added;                  /* 172 + 4         */
162 
+	%       int start_field;                 /* 176 + 4         */
163 
+	%       int field_skip;                  /* 180 + 4         */
164 
+	%       int omax;                        /* 184 + 4         */
165 
+	%       int omin;                        /* 188 + 4         */
166 
+	%       int smax;                        /* 192 + 4         */
167 
+	%       int smin;                        /* 196 + 4         */
168 
+	%       };                               /* total=200 bytes */
169 
+
170 
+   % descrip     = sprintf('%-80s', hist.descrip);     % 80 chars from left
171 
+   % fwrite(fid, descrip(1:80),    'uchar');
172 
+   pad = zeros(1, 80-length(hist.descrip));
173 
+   hist.descrip = [hist.descrip  char(pad)];
174 
+   fwrite(fid, hist.descrip(1:80), 'uchar');
175 
+
176 
+   % aux_file    = sprintf('%-24s', hist.aux_file);    % 24 chars from left
177 
+   % fwrite(fid, aux_file(1:24),   'uchar');
178 
+   pad = zeros(1, 24-length(hist.aux_file));
179 
+   hist.aux_file = [hist.aux_file  char(pad)];
180 
+   fwrite(fid, hist.aux_file(1:24), 'uchar');
181 
+
182 
+   fwrite(fid, hist.orient(1),      'uchar');
183 
+   fwrite(fid, hist.originator(1:5), 'int16');
184 
+
185 
+   pad = zeros(1, 10-length(hist.generated));
186 
+   hist.generated = [hist.generated  char(pad)];
187 
+   fwrite(fid, hist.generated(1:10),  'uchar');
188 
+
189 
+   pad = zeros(1, 10-length(hist.scannum));
190 
+   hist.scannum = [hist.scannum  char(pad)];
191 
+   fwrite(fid, hist.scannum(1:10),  'uchar');
192 
+
193 
+   pad = zeros(1, 10-length(hist.patient_id));
194 
+   hist.patient_id = [hist.patient_id  char(pad)];
195 
+   fwrite(fid, hist.patient_id(1:10),  'uchar');
196 
+
197 
+   pad = zeros(1, 10-length(hist.exp_date));
198 
+   hist.exp_date = [hist.exp_date  char(pad)];
199 
+   fwrite(fid, hist.exp_date(1:10),  'uchar');
200 
+
201 
+   pad = zeros(1, 10-length(hist.exp_time));
202 
+   hist.exp_time = [hist.exp_time  char(pad)];
203 
+   fwrite(fid, hist.exp_time(1:10),  'uchar');
204 
+
205 
+   pad = zeros(1, 3-length(hist.hist_un0));
206 
+   hist.hist_un0 = [hist.hist_un0  char(pad)];
207 
+   fwrite(fid, hist.hist_un0(1:3),  'uchar');
208 
+
209 
+   fwrite(fid, hist.views(1),      'int32');
210 
+   fwrite(fid, hist.vols_added(1), 'int32');
211 
+   fwrite(fid, hist.start_field(1),'int32');
212 
+   fwrite(fid, hist.field_skip(1), 'int32');
213 
+   fwrite(fid, hist.omax(1),       'int32');
214 
+   fwrite(fid, hist.omin(1),       'int32');
215 
+   fwrite(fid, hist.smax(1),       'int32');
216 
+   fwrite(fid, hist.smin(1),       'int32');
217 
+
218 
+   return;					% data_history
219 
+
NIFTI_20090325/save_untouch_nii.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,197 @@
1 
+%  Save NIFTI or ANALYZE dataset that is loaded by "load_untouch_nii.m".
2 
+%  The output image format and file extension will be the same as the
3 
+%  input one (NIFTI.nii, NIFTI.img or ANALYZE.img). Therefore, any file
4 
+%  extension that you specified will be ignored.
5 
+%
6 
+%  Usage: save_untouch_nii(nii, filename)
7 
+%
8 
+%  nii - nii structure that is loaded by "load_untouch_nii.m"
9 
+%
10 
+%  filename  - 	NIFTI or ANALYZE file name.
11 
+%
12 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
13 
+%
14 
+function save_untouch_nii(nii, filename)
15 
+
16 
+   if ~exist('nii','var') | isempty(nii) | ~isfield(nii,'hdr') | ...
17 
+	~isfield(nii,'img') | ~exist('filename','var') | isempty(filename)
18 
+
19 
+      error('Usage: save_untouch_nii(nii, filename)');
20 
+   end
21 
+
22 
+   if ~isfield(nii,'untouch') | nii.untouch == 0
23 
+      error('Usage: please use ''save_nii.m'' for the modified structure.');
24 
+   end
25 
+
26 
+   if isfield(nii.hdr.hist,'magic') & strcmp(nii.hdr.hist.magic(1:3),'ni1')
27 
+      filetype = 1;
28 
+   elseif isfield(nii.hdr.hist,'magic') & strcmp(nii.hdr.hist.magic(1:3),'n+1')
29 
+      filetype = 2;
30 
+   else
31 
+      filetype = 0;
32 
+   end
33 
+
34 
+   [p,f] = fileparts(filename);
35 
+   fileprefix = fullfile(p, f);
36 
+
37 
+   write_nii(nii, filetype, fileprefix);
38 
+
39 
+%   %  So earlier versions of SPM can also open it with correct originator
40 
+ %  %
41 
+  % if filetype == 0
42 
+   %   M=[[diag(nii.hdr.dime.pixdim(2:4)) -[nii.hdr.hist.originator(1:3).*nii.hdr.dime.pixdim(2:4)]'];[0 0 0 1]];
43 
+    %  save(fileprefix, 'M');
44 
+%   elseif filetype == 1
45 
+ %     M=[];
46 
+  %    save(fileprefix, 'M');
47 
+   %end
48 
+
49 
+   return					% save_untouch_nii
50 
+
51 
+
52 
+%-----------------------------------------------------------------------------------
53 
+function write_nii(nii, filetype, fileprefix)
54 
+
55 
+   hdr = nii.hdr;
56 
+
57 
+   if isfield(nii,'ext') & ~isempty(nii.ext)
58 
+      ext = nii.ext;
59 
+      [ext, esize_total] = verify_nii_ext(ext);
60 
+   else
61 
+      ext = [];
62 
+   end
63 
+
64 
+   switch double(hdr.dime.datatype),
65 
+   case   1,
66 
+      hdr.dime.bitpix = int16(1 ); precision = 'ubit1';
67 
+   case   2,
68 
+      hdr.dime.bitpix = int16(8 ); precision = 'uint8';
69 
+   case   4,
70 
+      hdr.dime.bitpix = int16(16); precision = 'int16';
71 
+   case   8,
72 
+      hdr.dime.bitpix = int16(32); precision = 'int32';
73 
+   case  16,
74 
+      hdr.dime.bitpix = int16(32); precision = 'float32';
75 
+   case  32,
76 
+      hdr.dime.bitpix = int16(64); precision = 'float32';
77 
+   case  64,
78 
+      hdr.dime.bitpix = int16(64); precision = 'float64';
79 
+   case 128,
80 
+      hdr.dime.bitpix = int16(24); precision = 'uint8';
81 
+   case 256
82 
+      hdr.dime.bitpix = int16(8 ); precision = 'int8';
83 
+   case 512
84 
+      hdr.dime.bitpix = int16(16); precision = 'uint16';
85 
+   case 768
86 
+      hdr.dime.bitpix = int16(32); precision = 'uint32';
87 
+   case 1024
88 
+      hdr.dime.bitpix = int16(64); precision = 'int64';
89 
+   case 1280
90 
+      hdr.dime.bitpix = int16(64); precision = 'uint64';
91 
+   case 1792,
92 
+      hdr.dime.bitpix = int16(128); precision = 'float64';
93 
+   otherwise
94 
+      error('This datatype is not supported');
95 
+   end
96 
+
97 
+%   hdr.dime.glmax = round(double(max(nii.img(:))));
98 
+ %  hdr.dime.glmin = round(double(min(nii.img(:))));
99 
+
100 
+   if filetype == 2
101 
+      fid = fopen(sprintf('%s.nii',fileprefix),'w');
102 
+
103 
+      if fid < 0,
104 
+         msg = sprintf('Cannot open file %s.nii.',fileprefix);
105 
+         error(msg);
106 
+      end
107 
+
108 
+      hdr.dime.vox_offset = 352;
109 
+
110 
+      if ~isempty(ext)
111 
+         hdr.dime.vox_offset = hdr.dime.vox_offset + esize_total;
112 
+      end
113 
+
114 
+      hdr.hist.magic = 'n+1';
115 
+      save_untouch_nii_hdr(hdr, fid);
116 
+
117 
+      if ~isempty(ext)
118 
+         save_nii_ext(ext, fid);
119 
+      end
120 
+   elseif filetype == 1
121 
+      fid = fopen(sprintf('%s.hdr',fileprefix),'w');
122 
+
123 
+      if fid < 0,
124 
+         msg = sprintf('Cannot open file %s.hdr.',fileprefix);
125 
+         error(msg);
126 
+      end
127 
+
128 
+      hdr.dime.vox_offset = 0;
129 
+      hdr.hist.magic = 'ni1';
130 
+      save_untouch_nii_hdr(hdr, fid);
131 
+
132 
+      if ~isempty(ext)
133 
+         save_nii_ext(ext, fid);
134 
+      end
135 
+
136 
+      fclose(fid);
137 
+      fid = fopen(sprintf('%s.img',fileprefix),'w');
138 
+   else
139 
+      fid = fopen(sprintf('%s.hdr',fileprefix),'w');
140 
+
141 
+      if fid < 0,
142 
+         msg = sprintf('Cannot open file %s.hdr.',fileprefix);
143 
+         error(msg);
144 
+      end
145 
+
146 
+      save_untouch0_nii_hdr(hdr, fid);
147 
+
148 
+      fclose(fid);
149 
+      fid = fopen(sprintf('%s.img',fileprefix),'w');
150 
+   end
151 
+
152 
+   ScanDim = double(hdr.dime.dim(5));		% t
153 
+   SliceDim = double(hdr.dime.dim(4));		% z
154 
+   RowDim   = double(hdr.dime.dim(3));		% y
155 
+   PixelDim = double(hdr.dime.dim(2));		% x
156 
+   SliceSz  = double(hdr.dime.pixdim(4));
157 
+   RowSz    = double(hdr.dime.pixdim(3));
158 
+   PixelSz  = double(hdr.dime.pixdim(2));
159 
+
160 
+   x = 1:PixelDim;
161 
+
162 
+   if filetype == 2 & isempty(ext)
163 
+      skip_bytes = double(hdr.dime.vox_offset) - 348;
164 
+   else
165 
+      skip_bytes = 0;
166 
+   end
167 
+
168 
+   if double(hdr.dime.datatype) == 128
169 
+
170 
+      %  RGB planes are expected to be in the 4th dimension of nii.img
171 
+      %
172 
+      if(size(nii.img,4)~=3)
173 
+         error(['The NII structure does not appear to have 3 RGB color planes in the 4th dimension']);
174 
+      end
175 
+
176 
+      nii.img = permute(nii.img, [4 1 2 3 5]);
177 
+   end
178 
+
179 
+   %  For complex float32 or complex float64, voxel values
180 
+   %  include [real, imag]
181 
+   %
182 
+   if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
183 
+      real_img = real(nii.img(:))';
184 
+      nii.img = imag(nii.img(:))';
185 
+      nii.img = [real_img; nii.img];
186 
+   end
187 
+
188 
+   if skip_bytes
189 
+      fwrite(fid, ones(1,skip_bytes), 'uint8');
190 
+   end
191 
+
192 
+   fwrite(fid, nii.img, precision);
193 
+%   fwrite(fid, nii.img, precision, skip_bytes);        % error using skip
194 
+   fclose(fid);
195 
+
196 
+   return;					% write_nii
197 
+
NIFTI_20090325/save_untouch_nii_hdr.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,207 @@
1 
+%  internal function
2 
+
3 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
4 
+
5 
+function save_nii_hdr(hdr, fid)
6 
+
7 
+   if ~isequal(hdr.hk.sizeof_hdr,348),
8 
+      error('hdr.hk.sizeof_hdr must be 348.');
9 
+   end
10 
+
11 
+   write_header(hdr, fid);
12 
+
13 
+   return;					% save_nii_hdr
14 
+
15 
+
16 
+%---------------------------------------------------------------------
17 
+function write_header(hdr, fid)
18 
+
19 
+        %  Original header structures
20 
+	%  struct dsr				/* dsr = hdr */
21 
+	%       {
22 
+	%       struct header_key hk;            /*   0 +  40       */
23 
+	%       struct image_dimension dime;     /*  40 + 108       */
24 
+	%       struct data_history hist;        /* 148 + 200       */
25 
+	%       };                               /* total= 348 bytes*/
26 
+
27 
+   header_key(fid, hdr.hk);
28 
+   image_dimension(fid, hdr.dime);
29 
+   data_history(fid, hdr.hist);
30 
+
31 
+   %  check the file size is 348 bytes
32 
+   %
33 
+   fbytes = ftell(fid);
34 
+
35 
+   if ~isequal(fbytes,348),
36 
+      msg = sprintf('Header size is not 348 bytes.');
37 
+      warning(msg);
38 
+   end
39 
+
40 
+   return;					% write_header
41 
+
42 
+
43 
+%---------------------------------------------------------------------
44 
+function header_key(fid, hk)
45 
+
46 
+   fseek(fid,0,'bof');
47 
+
48 
+	%  Original header structures
49 
+	%  struct header_key                      /* header key      */
50 
+	%       {                                /* off + size      */
51 
+	%       int sizeof_hdr                   /*  0 +  4         */
52 
+	%       char data_type[10];              /*  4 + 10         */
53 
+	%       char db_name[18];                /* 14 + 18         */
54 
+	%       int extents;                     /* 32 +  4         */
55 
+	%       short int session_error;         /* 36 +  2         */
56 
+	%       char regular;                    /* 38 +  1         */
57 
+	%       char dim_info;   % char hkey_un0;        /* 39 +  1 */
58 
+	%       };                               /* total=40 bytes  */
59 
+
60 
+   fwrite(fid, hk.sizeof_hdr(1),    'int32');	% must be 348.
61 
+
62 
+   % data_type = sprintf('%-10s',hk.data_type);	% ensure it is 10 chars from left
63 
+   % fwrite(fid, data_type(1:10), 'uchar');
64 
+   pad = zeros(1, 10-length(hk.data_type));
65 
+   hk.data_type = [hk.data_type  char(pad)];
66 
+   fwrite(fid, hk.data_type(1:10), 'uchar');
67 
+
68 
+   % db_name   = sprintf('%-18s', hk.db_name);	% ensure it is 18 chars from left
69 
+   % fwrite(fid, db_name(1:18), 'uchar');
70 
+   pad = zeros(1, 18-length(hk.db_name));
71 
+   hk.db_name = [hk.db_name  char(pad)];
72 
+   fwrite(fid, hk.db_name(1:18), 'uchar');
73 
+
74 
+   fwrite(fid, hk.extents(1),       'int32');
75 
+   fwrite(fid, hk.session_error(1), 'int16');
76 
+   fwrite(fid, hk.regular(1),       'uchar');	% might be uint8
77 
+
78 
+   % fwrite(fid, hk.hkey_un0(1),    'uchar');
79 
+   % fwrite(fid, hk.hkey_un0(1),    'uint8');
80 
+   fwrite(fid, hk.dim_info(1),      'uchar');
81 
+
82 
+   return;					% header_key
83 
+
84 
+
85 
+%---------------------------------------------------------------------
86 
+function image_dimension(fid, dime)
87 
+
88 
+	%  Original header structures
89 
+	%  struct image_dimension
90 
+	%       {                                /* off + size      */
91 
+	%       short int dim[8];                /* 0 + 16          */
92 
+	%       float intent_p1;   % char vox_units[4];   /* 16 + 4       */
93 
+	%       float intent_p2;   % char cal_units[8];   /* 20 + 4       */
94 
+	%       float intent_p3;   % char cal_units[8];   /* 24 + 4       */
95 
+	%       short int intent_code;   % short int unused1;   /* 28 + 2 */
96 
+	%       short int datatype;              /* 30 + 2          */
97 
+	%       short int bitpix;                /* 32 + 2          */
98 
+	%       short int slice_start;   % short int dim_un0;   /* 34 + 2 */
99 
+	%       float pixdim[8];                 /* 36 + 32         */
100 
+	%			/*
101 
+	%				pixdim[] specifies the voxel dimensions:
102 
+	%				pixdim[1] - voxel width
103 
+	%				pixdim[2] - voxel height
104 
+	%				pixdim[3] - interslice distance
105 
+	%				pixdim[4] - volume timing, in msec
106 
+	%					..etc
107 
+	%			*/
108 
+	%       float vox_offset;                /* 68 + 4          */
109 
+	%       float scl_slope;   % float roi_scale;     /* 72 + 4 */
110 
+	%       float scl_inter;   % float funused1;      /* 76 + 4 */
111 
+	%       short slice_end;   % float funused2;      /* 80 + 2 */
112 
+	%       char slice_code;   % float funused2;      /* 82 + 1 */
113 
+	%       char xyzt_units;   % float funused2;      /* 83 + 1 */
114 
+	%       float cal_max;                   /* 84 + 4          */
115 
+	%       float cal_min;                   /* 88 + 4          */
116 
+	%       float slice_duration;   % int compressed; /* 92 + 4 */
117 
+	%       float toffset;   % int verified;          /* 96 + 4 */
118 
+	%       int glmax;                       /* 100 + 4         */
119 
+	%       int glmin;                       /* 104 + 4         */
120 
+	%       };                               /* total=108 bytes */
121 
+
122 
+   fwrite(fid, dime.dim(1:8),        'int16');
123 
+   fwrite(fid, dime.intent_p1(1),  'float32');
124 
+   fwrite(fid, dime.intent_p2(1),  'float32');
125 
+   fwrite(fid, dime.intent_p3(1),  'float32');
126 
+   fwrite(fid, dime.intent_code(1),  'int16');
127 
+   fwrite(fid, dime.datatype(1),     'int16');
128 
+   fwrite(fid, dime.bitpix(1),       'int16');
129 
+   fwrite(fid, dime.slice_start(1),  'int16');
130 
+   fwrite(fid, dime.pixdim(1:8),   'float32');
131 
+   fwrite(fid, dime.vox_offset(1), 'float32');
132 
+   fwrite(fid, dime.scl_slope(1),  'float32');
133 
+   fwrite(fid, dime.scl_inter(1),  'float32');
134 
+   fwrite(fid, dime.slice_end(1),    'int16');
135 
+   fwrite(fid, dime.slice_code(1),   'uchar');
136 
+   fwrite(fid, dime.xyzt_units(1),   'uchar');
137 
+   fwrite(fid, dime.cal_max(1),    'float32');
138 
+   fwrite(fid, dime.cal_min(1),    'float32');
139 
+   fwrite(fid, dime.slice_duration(1), 'float32');
140 
+   fwrite(fid, dime.toffset(1),    'float32');
141 
+   fwrite(fid, dime.glmax(1),        'int32');
142 
+   fwrite(fid, dime.glmin(1),        'int32');
143 
+
144 
+   return;					% image_dimension
145 
+
146 
+
147 
+%---------------------------------------------------------------------
148 
+function data_history(fid, hist)
149 
+
150 
+	% Original header structures
151 
+	%struct data_history
152 
+	%       {                                /* off + size      */
153 
+	%       char descrip[80];                /* 0 + 80          */
154 
+	%       char aux_file[24];               /* 80 + 24         */
155 
+	%       short int qform_code;            /* 104 + 2         */
156 
+	%       short int sform_code;            /* 106 + 2         */
157 
+	%       float quatern_b;                 /* 108 + 4         */
158 
+	%       float quatern_c;                 /* 112 + 4         */
159 
+	%       float quatern_d;                 /* 116 + 4         */
160 
+	%       float qoffset_x;                 /* 120 + 4         */
161 
+	%       float qoffset_y;                 /* 124 + 4         */
162 
+	%       float qoffset_z;                 /* 128 + 4         */
163 
+	%       float srow_x[4];                 /* 132 + 16        */
164 
+	%       float srow_y[4];                 /* 148 + 16        */
165 
+	%       float srow_z[4];                 /* 164 + 16        */
166 
+	%       char intent_name[16];            /* 180 + 16        */
167 
+	%       char magic[4];   % int smin;     /* 196 + 4         */
168 
+	%       };                               /* total=200 bytes */
169 
+
170 
+   % descrip     = sprintf('%-80s', hist.descrip);     % 80 chars from left
171 
+   % fwrite(fid, descrip(1:80),    'uchar');
172 
+   pad = zeros(1, 80-length(hist.descrip));
173 
+   hist.descrip = [hist.descrip  char(pad)];
174 
+   fwrite(fid, hist.descrip(1:80), 'uchar');
175 
+
176 
+   % aux_file    = sprintf('%-24s', hist.aux_file);    % 24 chars from left
177 
+   % fwrite(fid, aux_file(1:24),   'uchar');
178 
+   pad = zeros(1, 24-length(hist.aux_file));
179 
+   hist.aux_file = [hist.aux_file  char(pad)];
180 
+   fwrite(fid, hist.aux_file(1:24), 'uchar');
181 
+
182 
+   fwrite(fid, hist.qform_code,    'int16');
183 
+   fwrite(fid, hist.sform_code,    'int16');
184 
+   fwrite(fid, hist.quatern_b,   'float32');
185 
+   fwrite(fid, hist.quatern_c,   'float32');
186 
+   fwrite(fid, hist.quatern_d,   'float32');
187 
+   fwrite(fid, hist.qoffset_x,   'float32');
188 
+   fwrite(fid, hist.qoffset_y,   'float32');
189 
+   fwrite(fid, hist.qoffset_z,   'float32');
190 
+   fwrite(fid, hist.srow_x(1:4), 'float32');
191 
+   fwrite(fid, hist.srow_y(1:4), 'float32');
192 
+   fwrite(fid, hist.srow_z(1:4), 'float32');
193 
+
194 
+   % intent_name = sprintf('%-16s', hist.intent_name);	% 16 chars from left
195 
+   % fwrite(fid, intent_name(1:16),    'uchar');
196 
+   pad = zeros(1, 16-length(hist.intent_name));
197 
+   hist.intent_name = [hist.intent_name  char(pad)];
198 
+   fwrite(fid, hist.intent_name(1:16), 'uchar');
199 
+
200 
+   % magic	= sprintf('%-4s', hist.magic);		% 4 chars from left
201 
+   % fwrite(fid, magic(1:4),           'uchar');
202 
+   pad = zeros(1, 4-length(hist.magic));
203 
+   hist.magic = [hist.magic  char(pad)];
204 
+   fwrite(fid, hist.magic(1:4),        'uchar');
205 
+
206 
+   return;					% data_history
207 
+
NIFTI_20090325/unxform_nii.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,40 @@
1 
+%  Undo the flipping and rotations performed by xform_nii; spit back only
2 
+%  the raw img data block. Initial cut will only deal with 3D volumes
3 
+%  strongly assume we have called xform_nii to write down the steps used
4 
+%  in xform_nii.
5 
+%
6 
+%  Usage:  a = load_nii('original_name');
7 
+%          manipulate a.img to make array b;
8 
+%
9 
+%          if you use unxform_nii to un-tranform the image (img) data
10 
+%          block, then nii.original.hdr is the corresponding header.
11 
+%
12 
+%          nii.original.img = unxform_nii(a, b);
13 
+%          save_nii(nii.original,'newname');
14 
+%
15 
+%  Where, 'newname' is created with data in the same space as the
16 
+%         original_name data
17 
+%
18 
+%  - Jeff Gunter, 26-JUN-06
19 
+%
20 
+function outblock = unxform_nii(nii, inblock)
21 
+
22 
+   if isempty(nii.hdr.hist.rot_orient)
23 
+      outblock=inblock;
24 
+   else
25 
+      [dummy unrotate_orient] = sort(nii.hdr.hist.rot_orient);
26 
+      outblock = permute(inblock, unrotate_orient);
27 
+   end
28 
+
29 
+   if ~isempty(nii.hdr.hist.flip_orient)
30 
+      flip_orient = nii.hdr.hist.flip_orient(unrotate_orient);
31 
+
32 
+      for i = 1:3
33 
+         if flip_orient(i)
34 
+            outblock = flipdim(outblock, i);
35 
+         end
36 
+      end
37 
+   end;
38 
+
39 
+   return;
40 
+
NIFTI_20090325/verify_nii_ext.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,45 @@
1 
+%  Verify NIFTI header extension to make sure that each extension section
2 
+%  must be an integer multiple of 16 byte long that includes the first 8
3 
+%  bytes of esize and ecode. If the length of extension section is not the
4 
+%  above mentioned case, edata should be padded with all 0.
5 
+%
6 
+%  Usage: [ext, esize_total] = verify_nii_ext(ext)
7 
+%
8 
+%  ext - Structure of NIFTI header extension, which includes num_ext,
9 
+%       and all the extended header sections in the header extension.
10 
+%       Each extended header section will have its esize, ecode, and
11 
+%       edata, where edata can be plain text, xml, or any raw data
12 
+%       that was saved in the extended header section.
13 
+%
14 
+%  esize_total - Sum of all esize variable in all header sections.
15 
+%
16 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
17 
+%
18 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
19 
+%
20 
+function [ext, esize_total] = verify_nii_ext(ext)
21 
+
22 
+   if ~isfield(ext, 'section')
23 
+      error('Incorrect NIFTI header extension structure.');
24 
+   elseif ~isfield(ext, 'num_ext')
25 
+      ext.num_ext = length(ext.section);
26 
+   elseif ~isfield(ext, 'extension')
27 
+      ext.extension = [1 0 0 0];
28 
+   end
29 
+
30 
+   esize_total = 0;
31 
+
32 
+   for i=1:ext.num_ext
33 
+      if ~isfield(ext.section(i), 'ecode') | ~isfield(ext.section(i), 'edata')
34 
+         error('Incorrect NIFTI header extension structure.');
35 
+      end
36 
+
37 
+      ext.section(i).esize = ceil((length(ext.section(i).edata)+8)/16)*16;
38 
+      ext.section(i).edata = ...
39 
+	[ext.section(i).edata ...
40 
+	 zeros(1,ext.section(i).esize-length(ext.section(i).edata)-8)];
41 
+      esize_total = esize_total + ext.section(i).esize;
42 
+   end
43 
+
44 
+   return                                       % verify_nii_ext
45 
+
NIFTI_20090325/view_nii.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,4847 @@
1 
+%  VIEW_NII: Create or update a 3-View (Front, Top, Side) of the
2 
+%	brain data that is specified by nii structure
3 
+%
4 
+%  Usage:  	status = view_nii([h], nii, [option])	or
5 
+%		status = view_nii(h, [option])
6 
+%
7 
+%  Where, h is the figure on which the 3-View will be plotted;
8 
+%	nii is the brain data in NIFTI format;
9 
+%	option is a struct that configures the view plotted, can be:
10 
+%
11 
+%		option.command = 'init'
12 
+%		option.command = 'update'
13 
+%		option.command = 'clearnii'
14 
+%		option.command = 'updatenii'
15 
+%		option.command = 'updateimg' (nii is nii.img here)
16 
+%
17 
+%		option.usecolorbar = 0 | [1]
18 
+%		option.usepanel = 0 | [1]
19 
+%		option.usecrosshair = 0 | [1]
20 
+%		option.usestretch = 0 | [1]
21 
+%		option.useimagesc = 0 | [1]
22 
+%		option.useinterp = [0] | 1
23 
+%
24 
+%		option.setarea = [x y w h] | [0.05 0.05 0.9 0.9]
25 
+%		option.setunit = ['vox'] | 'mm'
26 
+%		option.setviewpoint = [x y z] | [origin]
27 
+%		option.setscanid = [t] | [1]
28 
+%		option.setcrosshaircolor = [r g b] | [1 0 0]
29 
+%		option.setcolorindex = From 1 to 9 (default is 2 or 3)
30 
+%		option.setcolormap = (Mx3 matrix, 0 <= val <= 1)
31 
+%		option.setcolorlevel = No more than 256 (default 256)
32 
+%		option.sethighcolor = []
33 
+%		option.setcbarminmax = []
34 
+%		option.setvalue = []
35 
+%		option.glblocminmax = []
36 
+%		option.setbuttondown = ''
37 
+%		option.setcomplex = [0] | 1 | 2
38 
+%
39 
+%	Options description in detail:
40 
+%	==============================
41 
+%
42 
+%	1. command: A char string that can control program.
43 
+%
44 
+%		init: If option.command='init', the program will display
45 
+%			a 3-View plot on the figure specified by figure h
46 
+%			or on a new figure. If there is already a 3-View
47 
+%			plot on the figure, please use option.command =
48 
+%			'updatenii' (see detail below); otherwise, the
49 
+%			new 3-View plot will superimpose on the old one.
50 
+%			If there is no option provided, the program will
51 
+%			assume that this is an initial plot. If the figure
52 
+%			handle is omitted, the program knows that it is
53 
+%			an initial plot.
54 
+%
55 
+%		update: If there is no command specified, and a figure
56 
+%			handle of the existing 3-View plot is provided,
57 
+%			the program will choose option.command='update'
58 
+%			to update the 3-View plot with some new option
59 
+%			items.
60 
+%
61 
+%		clearnii: Clear 3-View plot on specific figure
62 
+%
63 
+%		updatenii: If a new nii is going to be loaded on a fig
64 
+%			that has already 3-View plot on it, use this
65 
+%			command to clear existing 3-View plot, and then
66 
+%			display with new nii. So, the new nii will not
67 
+%			superimpose on the existing one. All options
68 
+%			for 'init' can be used for 'updatenii'.
69 
+%
70 
+%		updateimg: If a new 3D matrix with the same dimension
71 
+%			is going to be loaded, option.command='updateimg'
72 
+%			can be used as a light-weighted 'updatenii, since
73 
+%			it only updates the 3 slices with new values.
74 
+%			inputing argument nii should be a 3D matrix
75 
+%			(nii.img) instead of nii struct. No other option
76 
+%			should be used together with 'updateimg' to keep
77 
+%			this command as simple as possible.
78 
+%
79 
+%
80 
+%	2. usecolorbar: If specified and usecolorbar=0, the program
81 
+%		will not include the colorbar in plot area; otherwise,
82 
+%		a colorbar will be included in plot area.
83 
+%
84 
+%	3. usepanel: If specified and usepanel=0, the control panel
85 
+%		at lower right cornor will be invisible; otherwise,
86 
+%		it will be visible.
87 
+%
88 
+%	4. usecrosshair: If specified and usecrosshair=0, the crosshair
89 
+%		will be invisible; otherwise, it will be visible.
90 
+%
91 
+%	5. usestretch: If specified and usestretch=0, the 3 slices will
92 
+%		not be stretched, and will be displayed according to
93 
+%		the actual voxel size; otherwise, the 3 slices will be
94 
+%		stretched to the edge.
95 
+%
96 
+%	6. useimagesc: If specified and useimagesc=0, images data will
97 
+%		be used directly to match the colormap (like 'image'
98 
+%		command); otherwise, image data will be scaled to full
99 
+%		colormap with 'imagesc' command in Matlab.
100 
+%
101 
+%	7. useinterp: If specified and useinterp=1, the image will be
102 
+%		displayed using interpolation. Otherwise, it will be
103 
+%		displayed like mosaic, and each tile stands for a
104 
+%		pixel. This option does not apply to 'setvalue' option
105 
+%		is set.
106 
+%
107 
+%
108 
+%	8. setarea: 3-View plot will be displayed on this specific
109 
+%		region. If it is not specified, program will set the
110 
+%		plot area to [0.05 0.05 0.9 0.9].
111 
+%
112 
+%	9. setunit: It can be specified to setunit='voxel' or 'mm'
113 
+%		and the view will change the axes unit of [X Y Z]
114 
+%		accordingly.
115 
+%
116 
+%	10. setviewpoint: If specified, [X Y Z] values will be used
117 
+%		to set the viewpoint of 3-View plot.
118 
+%
119 
+%	11. setscanid: If specified, [t] value will be used to display
120 
+%		the specified image scan in NIFTI data.
121 
+%
122 
+%	12. setcrosshaircolor: If specified, [r g b] value will be used
123 
+%		for Crosshair Color. Otherwise, red will be the default.
124 
+%
125 
+%	13. setcolorindex: If specified, the 3-View will choose the
126 
+%		following colormap:  2 - Bipolar; 3 - Gray; 4 - Jet;
127 
+%		5 - Cool; 6 - Bone; 7 - Hot; 8 - Copper; 9 - Pink;
128 
+%		If not specified, it will choose 3 - Gray if all data
129 
+%		values are not less than 0; otherwise, it will choose
130 
+%		2 - Bipolar if there is value less than 0. (Contrast
131 
+%		control can only apply to 3 - Gray colormap.
132 
+%
133 
+%	14. setcolormap: 3-View plot will use it as a customized colormap.
134 
+%		It is a 3-column matrix with value between 0 and 1. If
135 
+%		using MS-Windows version of Matlab, the number of rows
136 
+%		can not be more than 256, because of Matlab limitation.
137 
+%		When colormap is used, setcolorlevel option will be
138 
+%		disabled automatically.
139 
+%
140 
+%	15. setcolorlevel: If specified (must be no more than 256, and
141 
+%		cannot be used for customized colormap), row number of
142 
+%		colormap will be squeezed down to this level; otherwise,
143 
+%		it will assume that setcolorlevel=256.
144 
+%
145 
+%	16. sethighcolor: If specified, program will squeeze down the
146 
+%		colormap, and allocate sethighcolor (an Mx3 matrix)
147 
+%		to high-end portion of the colormap. The sum of M and
148 
+%		setcolorlevel should be less than 256. If setcolormap
149 
+%		option is used, sethighcolor will be inserted on top
150 
+%		of the setcolormap, and the setcolorlevel option will
151 
+%		be disabled automatically.
152 
+%
153 
+%	17. setcbarminmax: if specified, the [min max] will be used to
154 
+%		set the min and max of the colorbar, which does not
155 
+%		include any data for highcolor.
156 
+%
157 
+%	18. setvalue: If specified, setvalue.val (with the same size as
158 
+%		the source data on solution points) in the source area
159 
+%		setvalue.idx will be superimposed on the current nii
160 
+%		image. So, the size of setvalue.val should be equal to
161 
+%		the size of setvalue.idx. To use this feature, it needs
162 
+%		single or double nii structure for background image.
163 
+%
164 
+%	19. glblocminmax: If specified, pgm will use glblocminmax to
165 
+%		calculate the colormap, instead of minmax of image.
166 
+%
167 
+%	20. setbuttondown: If specified, pgm will evaluate the command
168 
+%		after a click or slide action is invoked to the new
169 
+%		view point.
170 
+%
171 
+%	21. setcomplex: This option will decide how complex data to be
172 
+%		displayed:  0 - Real part of complex data; 1 - Imaginary
173 
+%		part of complex data; 2 - Modulus (magnitude) of complex
174 
+%		data;  If not specified, it will be set to 0 (Real part
175 
+%		of complex data as default option. This option only apply
176 
+%		when option.command is set to 'init or 'updatenii'.
177 
+%
178 
+%
179 
+%	Additional Options for 'update' command:
180 
+%	=======================================
181 
+%
182 
+%		option.enablecursormove = [1] | 0
183 
+%		option.enableviewpoint = 0 | [1]
184 
+%		option.enableorigin = 0 | [1]
185 
+%		option.enableunit = 0 | [1]
186 
+%		option.enablecrosshair = 0 | [1]
187 
+%		option.enablehistogram = 0 | [1]
188 
+%		option.enablecolormap = 0 | [1]
189 
+%		option.enablecontrast = 0 | [1]
190 
+%		option.enablebrightness = 0 | [1]
191 
+%		option.enableslider = 0 | [1]
192 
+%		option.enabledirlabel = 0 | [1]
193 
+%
194 
+%
195 
+%  e.g.:
196 
+%	nii = load_nii('T1');		% T1.img/hdr
197 
+%	view_nii(nii);
198 
+%
199 
+%	or
200 
+%
201 
+%	h = figure('unit','normal','pos', [0.18 0.08 0.64 0.85]);
202 
+%	opt.setarea = [0.05 0.05 0.9 0.9];
203 
+%	view_nii(h, nii, opt);
204 
+%
205 
+%
206 
+%  Part of this file is copied and modified under GNU license from
207 
+%  MRI_TOOLBOX developed by CNSP in Flinders University, Australia
208 
+%
209 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
210 
+%
211 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
212 
+%
213 
+function status = view_nii(varargin)
214 
+
215 
+   if nargin < 1
216 
+      error('Please check inputs using ''help view_nii''');
217 
+   end;
218 
+
219 
+   nii = '';
220 
+   opt = '';
221 
+   command = '';
222 
+
223 
+   usecolorbar = [];
224 
+   usepanel = [];
225 
+   usecrosshair = '';
226 
+   usestretch = [];
227 
+   useimagesc = [];
228 
+   useinterp = [];
229 
+
230 
+   setarea = [];
231 
+   setunit = '';
232 
+   setviewpoint = [];
233 
+   setscanid = [];
234 
+   setcrosshaircolor = [];
235 
+   setcolorindex = '';
236 
+   setcolormap = 'NA';
237 
+   setcolorlevel = [];
238 
+   sethighcolor = 'NA';
239 
+   setcbarminmax = [];
240 
+   setvalue = [];
241 
+   glblocminmax = [];
242 
+   setbuttondown = '';
243 
+   setcomplex = 0;
244 
+
245 
+   status = [];
246 
+
247 
+   if ishandle(varargin{1})		% plot on top of this figure
248 
+
249 
+      fig = varargin{1};
250 
+
251 
+      if nargin < 2
252 
+         command = 'update';		% just to get 3-View status
253 
+      end
254 
+
255 
+      if nargin == 2
256 
+         if ~isstruct(varargin{2})
257 
+            error('2nd parameter should be either nii struct or option struct');
258 
+         end
259 
+
260 
+         opt = varargin{2};
261 
+
262 
+         if isfield(opt,'hdr') & isfield(opt,'img')
263 
+            nii = opt;
264 
+         elseif isfield(opt, 'command') & (strcmpi(opt.command,'init') ...
265 
+		| strcmpi(opt.command,'updatenii') ...
266 
+		| strcmpi(opt.command,'updateimg') )
267 
+
268 
+            error('Option here cannot contain "init", "updatenii", or "updateimg" comand');
269 
+         end
270 
+      end
271 
+
272 
+      if nargin == 3
273 
+         nii = varargin{2};
274 
+         opt = varargin{3};
275 
+
276 
+         if ~isstruct(opt)
277 
+            error('3rd parameter should be option struct');
278 
+         end
279 
+
280 
+         if ~isfield(opt,'command') | ~strcmpi(opt.command,'updateimg')
281 
+            if ~isstruct(nii) | ~isfield(nii,'hdr') | ~isfield(nii,'img')
282 
+               error('2nd parameter should be nii struct');
283 
+            end
284 
+
285 
+            if isfield(nii,'untouch') & nii.untouch == 1
286 
+               error('Usage: please use ''load_nii.m'' to load the structure.');
287 
+            end
288 
+         end
289 
+      end
290 
+
291 
+      set(fig, 'menubar', 'none');
292 
+
293 
+   elseif ischar(varargin{1})		% call back by event
294 
+
295 
+      command = lower(varargin{1});
296 
+      fig = gcbf;
297 
+
298 
+   else					% start nii with a new figure
299 
+
300 
+      nii = varargin{1};
301 
+
302 
+      if ~isstruct(nii) | ~isfield(nii,'hdr') | ~isfield(nii,'img')
303 
+         error('1st parameter should be either a figure handle or nii struct');
304 
+      end
305 
+
306 
+      if isfield(nii,'untouch') & nii.untouch == 1
307 
+         error('Usage: please use ''load_nii.m'' to load the structure.');
308 
+      end
309 
+
310 
+      if nargin > 1
311 
+         opt = varargin{2};
312 
+
313 
+         if isfield(opt, 'command') & ~strcmpi(opt.command,'init')
314 
+            error('Option here must use "init" comand');
315 
+         end
316 
+      end
317 
+
318 
+      command = 'init';
319 
+      fig = figure('unit','normal','position',[0.15 0.08 0.70 0.85]);
320 
+      view_nii_menu(fig);
321 
+      rri_file_menu(fig);
322 
+
323 
+   end
324 
+
325 
+   if ~isempty(opt)
326 
+
327 
+      if isfield(opt,'command')
328 
+         command = lower(opt.command);
329 
+      end
330 
+
331 
+      if isempty(command)
332 
+         command = 'update';
333 
+      end
334 
+
335 
+      if isfield(opt,'usecolorbar')
336 
+         usecolorbar = opt.usecolorbar;
337 
+      end
338 
+
339 
+      if isfield(opt,'usepanel')
340 
+         usepanel = opt.usepanel;
341 
+      end
342 
+
343 
+      if isfield(opt,'usecrosshair')
344 
+         usecrosshair = opt.usecrosshair;
345 
+      end
346 
+
347 
+      if isfield(opt,'usestretch')
348 
+         usestretch = opt.usestretch;
349 
+      end
350 
+
351 
+      if isfield(opt,'useimagesc')
352 
+         useimagesc = opt.useimagesc;
353 
+      end
354 
+
355 
+      if isfield(opt,'useinterp')
356 
+         useinterp = opt.useinterp;
357 
+      end
358 
+
359 
+      if isfield(opt,'setarea')
360 
+         setarea = opt.setarea;
361 
+      end
362 
+
363 
+      if isfield(opt,'setunit')
364 
+         setunit = opt.setunit;
365 
+      end
366 
+
367 
+      if isfield(opt,'setviewpoint')
368 
+         setviewpoint = opt.setviewpoint;
369 
+      end
370 
+
371 
+      if isfield(opt,'setscanid')
372 
+         setscanid = opt.setscanid;
373 
+      end
374 
+
375 
+      if isfield(opt,'setcrosshaircolor')
376 
+         setcrosshaircolor = opt.setcrosshaircolor;
377 
+
378 
+         if ~isempty(setcrosshaircolor) & (~isnumeric(setcrosshaircolor) | ~isequal(size(setcrosshaircolor),[1 3]) | min(setcrosshaircolor(:))<0 | max(setcrosshaircolor(:))>1)
379 
+            error('Crosshair Color should be a 1x3 matrix with value between 0 and 1');
380 
+         end
381 
+      end
382 
+
383 
+      if isfield(opt,'setcolorindex')
384 
+         setcolorindex = round(opt.setcolorindex);
385 
+
386 
+         if ~isnumeric(setcolorindex) | setcolorindex < 1 | setcolorindex > 9
387 
+            error('Colorindex should be a number between 1 and 9');
388 
+         end
389 
+      end
390 
+
391 
+      if isfield(opt,'setcolormap')
392 
+         setcolormap = opt.setcolormap;
393 
+
394 
+         if ~isempty(setcolormap) & (~isnumeric(setcolormap) | size(setcolormap,2) ~= 3 | min(setcolormap(:))<0 | max(setcolormap(:))>1)
395 
+            error('Colormap should be a Mx3 matrix with value between 0 and 1');
396 
+         end
397 
+      end
398 
+
399 
+      if isfield(opt,'setcolorlevel')
400 
+         setcolorlevel = round(opt.setcolorlevel);
401 
+
402 
+         if ~isnumeric(setcolorlevel) | setcolorlevel > 256 | setcolorlevel < 1
403 
+            error('Colorlevel should be a number between 1 and 256');
404 
+         end
405 
+      end
406 
+
407 
+      if isfield(opt,'sethighcolor')
408 
+         sethighcolor = opt.sethighcolor;
409 
+
410 
+         if ~isempty(sethighcolor) & (~isnumeric(sethighcolor) | size(sethighcolor,2) ~= 3 | min(sethighcolor(:))<0 | max(sethighcolor(:))>1)
411 
+            error('Highcolor should be a Mx3 matrix with value between 0 and 1');
412 
+         end
413 
+      end
414 
+
415 
+      if isfield(opt,'setcbarminmax')
416 
+         setcbarminmax = opt.setcbarminmax;
417 
+
418 
+         if isempty(setcbarminmax) | ~isnumeric(setcbarminmax) | length(setcbarminmax) ~= 2
419 
+            error('Colorbar MinMax should contain 2 values: [min max]');
420 
+         end
421 
+      end
422 
+
423 
+      if isfield(opt,'setvalue')
424 
+         setvalue = opt.setvalue;
425 
+
426 
+         if isempty(setvalue) | ~isstruct(setvalue) | ...
427 
+		~isfield(opt.setvalue,'idx') | ~isfield(opt.setvalue,'val')
428 
+            error('setvalue should be a struct contains idx and val');
429 
+         end
430 
+
431 
+         if length(opt.setvalue.idx(:)) ~= length(opt.setvalue.val(:))
432 
+            error('length of idx and val fields should be the same');
433 
+         end
434 
+
435 
+         if ~strcmpi(class(opt.setvalue.idx),'single')
436 
+            opt.setvalue.idx = single(opt.setvalue.idx);
437 
+         end
438 
+
439 
+         if ~strcmpi(class(opt.setvalue.val),'single')
440 
+            opt.setvalue.val = single(opt.setvalue.val);
441 
+         end
442 
+      end
443 
+
444 
+      if isfield(opt,'glblocminmax')
445 
+         glblocminmax = opt.glblocminmax;
446 
+      end
447 
+
448 
+      if isfield(opt,'setbuttondown')
449 
+         setbuttondown = opt.setbuttondown;
450 
+      end
451 
+
452 
+      if isfield(opt,'setcomplex')
453 
+         setcomplex = opt.setcomplex;
454 
+      end
455 
+
456 
+   end
457 
+
458 
+   switch command
459 
+
460 
+   case {'init'}
461 
+
462 
+      set(fig, 'InvertHardcopy','off');
463 
+      set(fig, 'PaperPositionMode','auto');
464 
+
465 
+      fig = init(nii, fig, setarea, setunit, setviewpoint, setscanid, setbuttondown, ...
466 
+         setcolorindex, setcolormap, setcolorlevel, sethighcolor, setcbarminmax, ...
467 
+         usecolorbar, usepanel, usecrosshair, usestretch, useimagesc, useinterp, ...
468 
+         setvalue, glblocminmax, setcrosshaircolor, setcomplex);
469 
+
470 
+      %  get status
471 
+      %
472 
+      status = get_status(fig);
473 
+
474 
+   case {'update'}
475 
+
476 
+      nii_view = getappdata(fig,'nii_view');
477 
+      h = fig;
478 
+
479 
+      if isempty(nii_view)
480 
+         error('The figure should already contain a 3-View plot.');
481 
+      end
482 
+
483 
+      if ~isempty(opt)
484 
+
485 
+         %  Order of the following update matters.
486 
+         %
487 
+         update_shape(h, setarea, usecolorbar, usestretch, useimagesc);
488 
+         update_useinterp(h, useinterp);
489 
+         update_useimagesc(h, useimagesc);
490 
+         update_usepanel(h, usepanel);
491 
+         update_colorindex(h, setcolorindex);
492 
+         update_colormap(h, setcolormap);
493 
+         update_highcolor(h, sethighcolor, setcolorlevel);
494 
+         update_cbarminmax(h, setcbarminmax);
495 
+         update_unit(h, setunit);
496 
+         update_viewpoint(h, setviewpoint);
497 
+         update_scanid(h, setscanid);
498 
+         update_buttondown(h, setbuttondown);
499 
+         update_crosshaircolor(h, setcrosshaircolor);
500 
+         update_usecrosshair(h, usecrosshair);
501 
+
502 
+         %  Enable/Disable object
503 
+         %
504 
+         update_enable(h, opt);
505 
+
506 
+      end
507 
+
508 
+      %  get status
509 
+      %
510 
+      status = get_status(h);
511 
+
512 
+   case {'updateimg'}
513 
+
514 
+      if ~exist('nii','var')
515 
+         msg = sprintf('Please input a 3D matrix brain data');
516 
+         error(msg);
517 
+      end
518 
+
519 
+      %  Note: nii is not nii, nii should be a 3D matrix here
520 
+      %
521 
+      if ~isnumeric(nii)
522 
+         msg = sprintf('2nd parameter should be a 3D matrix, not nii struct');
523 
+         error(msg);
524 
+      end
525 
+
526 
+      nii_view = getappdata(fig,'nii_view');
527 
+
528 
+      if isempty(nii_view)
529 
+         error('The figure should already contain a 3-View plot.');
530 
+      end
531 
+
532 
+      img = nii;
533 
+      update_img(img, fig, opt);
534 
+
535 
+      %  get status
536 
+      %
537 
+      status = get_status(fig);
538 
+
539 
+   case {'updatenii'}
540 
+
541 
+      nii_view = getappdata(fig,'nii_view');
542 
+
543 
+      if isempty(nii_view)
544 
+         error('The figure should already contain a 3-View plot.');
545 
+      end
546 
+
547 
+      if ~isstruct(nii) | ~isfield(nii,'hdr') | ~isfield(nii,'img')
548 
+         error('2nd parameter should be nii struct');
549 
+      end
550 
+
551 
+      if isfield(nii,'untouch') & nii.untouch == 1
552 
+         error('Usage: please use ''load_nii.m'' to load the structure.');
553 
+      end
554 
+
555 
+      opt.command = 'clearnii';
556 
+      view_nii(fig, opt);
557 
+
558 
+      opt.command = 'init';
559 
+      view_nii(fig, nii, opt);
560 
+
561 
+      %  get status
562 
+      %
563 
+      status = get_status(fig);
564 
+
565 
+   case {'clearnii'}
566 
+
567 
+      nii_view = getappdata(fig,'nii_view');
568 
+
569 
+      handles = struct2cell(nii_view.handles);
570 
+
571 
+      for i=1:length(handles)
572 
+         if ishandle(handles{i})	% in case already del by parent
573 
+            delete(handles{i});
574 
+         end
575 
+      end
576 
+
577 
+      rmappdata(fig,'nii_view');
578 
+      buttonmotion = get(fig,'windowbuttonmotion');
579 
+      mymotion = '; view_nii(''move_cursor'');';
580 
+      buttonmotion = strrep(buttonmotion, mymotion, '');
581 
+      set(fig, 'windowbuttonmotion', buttonmotion);
582 
+
583 
+   case {'axial_image','coronal_image','sagittal_image'}
584 
+
585 
+      switch command
586 
+         case 'axial_image',    view = 'axi'; axi = 0; cor = 1; sag = 1;
587 
+         case 'coronal_image',  view = 'cor'; axi = 1; cor = 0; sag = 1;
588 
+         case 'sagittal_image', view = 'sag'; axi = 1; cor = 1; sag = 0;
589 
+      end
590 
+
591 
+      nii_view = getappdata(fig,'nii_view');
592 
+      nii_view = get_slice_position(nii_view,view);
593 
+
594 
+      if isfield(nii_view, 'disp')
595 
+         img = nii_view.disp;
596 
+      else
597 
+         img = nii_view.nii.img;
598 
+      end
599 
+
600 
+      %  CData must be double() for Matlab 6.5 for Windows
601 
+      %
602 
+      if axi,
603 
+         if isfield(nii_view.handles,'axial_bg') & ~isempty(nii_view.handles.axial_bg) & nii_view.useinterp
604 
+            Saxi = squeeze(nii_view.bgimg(:,:,nii_view.slices.axi));
605 
+            set(nii_view.handles.axial_bg,'CData',Saxi');
606 
+         end
607 
+
608 
+         if isfield(nii_view.handles,'axial_image'),
609 
+            if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
610 
+               Saxi = squeeze(img(:,:,nii_view.slices.axi,:,nii_view.scanid));
611 
+               Saxi = permute(Saxi, [2 1 3]);
612 
+            else
613 
+               Saxi = squeeze(img(:,:,nii_view.slices.axi,nii_view.scanid));
614 
+               Saxi = Saxi';
615 
+            end
616 
+
617 
+            set(nii_view.handles.axial_image,'CData',Saxi);
618 
+         end
619 
+
620 
+         if isfield(nii_view.handles,'axial_slider'),
621 
+            set(nii_view.handles.axial_slider,'Value',nii_view.slices.axi);
622 
+         end;
623 
+       end
624 
+
625 
+       if cor,
626 
+         if isfield(nii_view.handles,'coronal_bg') & ~isempty(nii_view.handles.coronal_bg) & nii_view.useinterp
627 
+            Scor = squeeze(nii_view.bgimg(:,nii_view.slices.cor,:));
628 
+            set(nii_view.handles.coronal_bg,'CData',Scor');
629 
+         end
630 
+
631 
+         if isfield(nii_view.handles,'coronal_image'),
632 
+            if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
633 
+               Scor = squeeze(img(:,nii_view.slices.cor,:,:,nii_view.scanid));
634 
+               Scor = permute(Scor, [2 1 3]);
635 
+            else
636 
+               Scor = squeeze(img(:,nii_view.slices.cor,:,nii_view.scanid));
637 
+               Scor = Scor';
638 
+            end
639 
+
640 
+            set(nii_view.handles.coronal_image,'CData',Scor);
641 
+         end
642 
+
643 
+         if isfield(nii_view.handles,'coronal_slider'),
644 
+            slider_val = nii_view.dims(2) - nii_view.slices.cor + 1;
645 
+            set(nii_view.handles.coronal_slider,'Value',slider_val);
646 
+         end;
647 
+      end;
648 
+
649 
+      if sag,
650 
+         if isfield(nii_view.handles,'sagittal_bg') & ~isempty(nii_view.handles.sagittal_bg) & nii_view.useinterp
651 
+            Ssag = squeeze(nii_view.bgimg(nii_view.slices.sag,:,:));
652 
+            set(nii_view.handles.sagittal_bg,'CData',Ssag');
653 
+         end
654 
+
655 
+         if isfield(nii_view.handles,'sagittal_image'),
656 
+            if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
657 
+               Ssag = squeeze(img(nii_view.slices.sag,:,:,:,nii_view.scanid));
658 
+               Ssag = permute(Ssag, [2 1 3]);
659 
+            else
660 
+               Ssag = squeeze(img(nii_view.slices.sag,:,:,nii_view.scanid));
661 
+               Ssag = Ssag';
662 
+            end
663 
+
664 
+            set(nii_view.handles.sagittal_image,'CData',Ssag);
665 
+         end
666 
+
667 
+         if isfield(nii_view.handles,'sagittal_slider'),
668 
+            set(nii_view.handles.sagittal_slider,'Value',nii_view.slices.sag);
669 
+         end;
670 
+      end;
671 
+
672 
+      update_nii_view(nii_view);
673 
+
674 
+      if ~isempty(nii_view.buttondown)
675 
+         eval(nii_view.buttondown);
676 
+      end
677 
+
678 
+   case {'axial_slider','coronal_slider','sagittal_slider'},
679 
+
680 
+      switch command
681 
+         case 'axial_slider',    view = 'axi'; axi = 1; cor = 0; sag = 0;
682 
+         case 'coronal_slider',  view = 'cor'; axi = 0; cor = 1; sag = 0;
683 
+         case 'sagittal_slider', view = 'sag'; axi = 0; cor = 0; sag = 1;
684 
+      end
685 
+
686 
+      nii_view = getappdata(fig,'nii_view');
687 
+      nii_view = get_slider_position(nii_view);
688 
+
689 
+      if isfield(nii_view, 'disp')
690 
+         img = nii_view.disp;
691 
+      else
692 
+         img = nii_view.nii.img;
693 
+      end
694 
+
695 
+      if axi,
696 
+         if isfield(nii_view.handles,'axial_bg') & ~isempty(nii_view.handles.axial_bg) & nii_view.useinterp
697 
+            Saxi = squeeze(nii_view.bgimg(:,:,nii_view.slices.axi));
698 
+            set(nii_view.handles.axial_bg,'CData',Saxi');
699 
+         end
700 
+
701 
+         if isfield(nii_view.handles,'axial_image'),
702 
+            if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
703 
+               Saxi = squeeze(img(:,:,nii_view.slices.axi,:,nii_view.scanid));
704 
+               Saxi = permute(Saxi, [2 1 3]);
705 
+            else
706 
+               Saxi = squeeze(img(:,:,nii_view.slices.axi,nii_view.scanid));
707 
+               Saxi = Saxi';
708 
+            end
709 
+
710 
+            set(nii_view.handles.axial_image,'CData',Saxi);
711 
+         end
712 
+
713 
+         if isfield(nii_view.handles,'axial_slider'),
714 
+            set(nii_view.handles.axial_slider,'Value',nii_view.slices.axi);
715 
+         end
716 
+      end
717 
+
718 
+      if cor,
719 
+         if isfield(nii_view.handles,'coronal_bg') & ~isempty(nii_view.handles.coronal_bg) & nii_view.useinterp
720 
+            Scor = squeeze(nii_view.bgimg(:,nii_view.slices.cor,:));
721 
+            set(nii_view.handles.coronal_bg,'CData',Scor');
722 
+         end
723 
+
724 
+         if isfield(nii_view.handles,'coronal_image'),
725 
+            if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
726 
+               Scor = squeeze(img(:,nii_view.slices.cor,:,:,nii_view.scanid));
727 
+               Scor = permute(Scor, [2 1 3]);
728 
+            else
729 
+               Scor = squeeze(img(:,nii_view.slices.cor,:,nii_view.scanid));
730 
+               Scor = Scor';
731 
+            end
732 
+
733 
+            set(nii_view.handles.coronal_image,'CData',Scor);
734 
+         end
735 
+
736 
+         if isfield(nii_view.handles,'coronal_slider'),
737 
+            slider_val = nii_view.dims(2) - nii_view.slices.cor + 1;
738 
+            set(nii_view.handles.coronal_slider,'Value',slider_val);
739 
+         end
740 
+      end
741 
+
742 
+      if sag,
743 
+         if isfield(nii_view.handles,'sagittal_bg') & ~isempty(nii_view.handles.sagittal_bg) & nii_view.useinterp
744 
+            Ssag = squeeze(nii_view.bgimg(nii_view.slices.sag,:,:));
745 
+            set(nii_view.handles.sagittal_bg,'CData',Ssag');
746 
+         end
747 
+
748 
+         if isfield(nii_view.handles,'sagittal_image'),
749 
+            if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
750 
+               Ssag = squeeze(img(nii_view.slices.sag,:,:,:,nii_view.scanid));
751 
+               Ssag = permute(Ssag, [2 1 3]);
752 
+            else
753 
+               Ssag = squeeze(img(nii_view.slices.sag,:,:,nii_view.scanid));
754 
+               Ssag = Ssag';
755 
+            end
756 
+
757 
+            set(nii_view.handles.sagittal_image,'CData',Ssag);
758 
+         end
759 
+
760 
+         if isfield(nii_view.handles,'sagittal_slider'),
761 
+            set(nii_view.handles.sagittal_slider,'Value',nii_view.slices.sag);
762 
+         end
763 
+      end
764 
+
765 
+      update_nii_view(nii_view);
766 
+
767 
+      if ~isempty(nii_view.buttondown)
768 
+         eval(nii_view.buttondown);
769 
+      end
770 
+
771 
+   case {'impos_edit'}
772 
+
773 
+      nii_view = getappdata(fig,'nii_view');
774 
+      impos = str2num(get(nii_view.handles.impos,'string'));
775 
+
776 
+      if isfield(nii_view, 'disp')
777 
+         img = nii_view.disp;
778 
+      else
779 
+         img = nii_view.nii.img;
780 
+      end
781 
+
782 
+      if isempty(impos) | ~all(size(impos) ==  [1 3])
783 
+         msg = 'Please use 3 numbers to represent X,Y and Z';
784 
+         msgbox(msg,'Error');
785 
+         return;
786 
+      end
787 
+
788 
+      slices.sag = round(impos(1));
789 
+      slices.cor = round(impos(2));
790 
+      slices.axi = round(impos(3));
791 
+
792 
+      nii_view = convert2voxel(nii_view,slices);
793 
+      nii_view = check_slices(nii_view);
794 
+
795 
+      impos(1) = nii_view.slices.sag;
796 
+      impos(2) = nii_view.dims(2) - nii_view.slices.cor + 1;
797 
+      impos(3) = nii_view.slices.axi;
798 
+
799 
+      if isfield(nii_view.handles,'sagittal_slider'),
800 
+         set(nii_view.handles.sagittal_slider,'Value',impos(1));
801 
+      end
802 
+
803 
+      if isfield(nii_view.handles,'coronal_slider'),
804 
+         set(nii_view.handles.coronal_slider,'Value',impos(2));
805 
+      end
806 
+
807 
+      if isfield(nii_view.handles,'axial_slider'),
808 
+         set(nii_view.handles.axial_slider,'Value',impos(3));
809 
+      end
810 
+
811 
+      nii_view = get_slider_position(nii_view);
812 
+      update_nii_view(nii_view);
813 
+
814 
+      if isfield(nii_view.handles,'axial_bg') & ~isempty(nii_view.handles.axial_bg) & nii_view.useinterp
815 
+         Saxi = squeeze(nii_view.bgimg(:,:,nii_view.slices.axi));
816 
+         set(nii_view.handles.axial_bg,'CData',Saxi');
817 
+      end
818 
+
819 
+      if isfield(nii_view.handles,'axial_image'),
820 
+         if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
821 
+            Saxi = squeeze(img(:,:,nii_view.slices.axi,:,nii_view.scanid));
822 
+            Saxi = permute(Saxi, [2 1 3]);
823 
+         else
824 
+            Saxi = squeeze(img(:,:,nii_view.slices.axi,nii_view.scanid));
825 
+            Saxi = Saxi';
826 
+         end
827 
+
828 
+         set(nii_view.handles.axial_image,'CData',Saxi);
829 
+      end
830 
+
831 
+      if isfield(nii_view.handles,'axial_slider'),
832 
+         set(nii_view.handles.axial_slider,'Value',nii_view.slices.axi);
833 
+      end
834 
+
835 
+      if isfield(nii_view.handles,'coronal_bg') & ~isempty(nii_view.handles.coronal_bg) & nii_view.useinterp
836 
+         Scor = squeeze(nii_view.bgimg(:,nii_view.slices.cor,:));
837 
+         set(nii_view.handles.coronal_bg,'CData',Scor');
838 
+      end
839 
+
840 
+      if isfield(nii_view.handles,'coronal_image'),
841 
+         if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
842 
+            Scor = squeeze(img(:,nii_view.slices.cor,:,:,nii_view.scanid));
843 
+            Scor = permute(Scor, [2 1 3]);
844 
+         else
845 
+            Scor = squeeze(img(:,nii_view.slices.cor,:,nii_view.scanid));
846 
+            Scor = Scor';
847 
+         end
848 
+
849 
+         set(nii_view.handles.coronal_image,'CData',Scor);
850 
+      end
851 
+
852 
+      if isfield(nii_view.handles,'coronal_slider'),
853 
+         slider_val = nii_view.dims(2) - nii_view.slices.cor + 1;
854 
+         set(nii_view.handles.coronal_slider,'Value',slider_val);
855 
+      end
856 
+
857 
+      if isfield(nii_view.handles,'sagittal_bg') & ~isempty(nii_view.handles.sagittal_bg) & nii_view.useinterp
858 
+         Ssag = squeeze(nii_view.bgimg(nii_view.slices.sag,:,:));
859 
+         set(nii_view.handles.sagittal_bg,'CData',Ssag');
860 
+      end
861 
+
862 
+      if isfield(nii_view.handles,'sagittal_image'),
863 
+         if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
864 
+            Ssag = squeeze(img(nii_view.slices.sag,:,:,:,nii_view.scanid));
865 
+            Ssag = permute(Ssag, [2 1 3]);
866 
+         else
867 
+            Ssag = squeeze(img(nii_view.slices.sag,:,:,nii_view.scanid));
868 
+            Ssag = Ssag';
869 
+         end
870 
+
871 
+         set(nii_view.handles.sagittal_image,'CData',Ssag);
872 
+      end
873 
+
874 
+      if isfield(nii_view.handles,'sagittal_slider'),
875 
+         set(nii_view.handles.sagittal_slider,'Value',nii_view.slices.sag);
876 
+      end
877 
+
878 
+      axes(nii_view.handles.axial_axes);
879 
+      axes(nii_view.handles.coronal_axes);
880 
+      axes(nii_view.handles.sagittal_axes);
881 
+
882 
+      if ~isempty(nii_view.buttondown)
883 
+         eval(nii_view.buttondown);
884 
+      end
885 
+
886 
+   case 'coordinates',
887 
+
888 
+      nii_view = getappdata(fig,'nii_view');
889 
+      set_image_value(nii_view);
890 
+
891 
+   case 'crosshair',
892 
+
893 
+      nii_view = getappdata(fig,'nii_view');
894 
+
895 
+      if get(nii_view.handles.xhair,'value') == 2		% off
896 
+         set(nii_view.axi_xhair.lx,'visible','off');
897 
+         set(nii_view.axi_xhair.ly,'visible','off');
898 
+         set(nii_view.cor_xhair.lx,'visible','off');
899 
+         set(nii_view.cor_xhair.ly,'visible','off');
900 
+         set(nii_view.sag_xhair.lx,'visible','off');
901 
+         set(nii_view.sag_xhair.ly,'visible','off');
902 
+      else
903 
+         set(nii_view.axi_xhair.lx,'visible','on');
904 
+         set(nii_view.axi_xhair.ly,'visible','on');
905 
+         set(nii_view.cor_xhair.lx,'visible','on');
906 
+         set(nii_view.cor_xhair.ly,'visible','on');
907 
+         set(nii_view.sag_xhair.lx,'visible','on');
908 
+         set(nii_view.sag_xhair.ly,'visible','on');
909 
+
910 
+         set(nii_view.handles.axial_axes,'selected','on');
911 
+         set(nii_view.handles.axial_axes,'selected','off');
912 
+         set(nii_view.handles.coronal_axes,'selected','on');
913 
+         set(nii_view.handles.coronal_axes,'selected','off');
914 
+         set(nii_view.handles.sagittal_axes,'selected','on');
915 
+         set(nii_view.handles.sagittal_axes,'selected','off');
916 
+      end
917 
+
918 
+   case 'xhair_color',
919 
+
920 
+      old_color = get(gcbo,'user');
921 
+      new_color = uisetcolor(old_color);
922 
+      update_crosshaircolor(fig, new_color);
923 
+
924 
+   case {'color','contrast_def'}
925 
+
926 
+      nii_view = getappdata(fig,'nii_view');
927 
+
928 
+      if nii_view.numscan == 1
929 
+         if get(nii_view.handles.colorindex,'value') == 2
930 
+            set(nii_view.handles.contrast,'value',128);
931 
+         elseif get(nii_view.handles.colorindex,'value') == 3
932 
+            set(nii_view.handles.contrast,'value',1);
933 
+         end
934 
+      end
935 
+
936 
+      [custom_color_map, custom_colorindex] = change_colormap(fig);
937 
+
938 
+      if strcmpi(command, 'color')
939 
+
940 
+         setcolorlevel = nii_view.colorlevel;
941 
+
942 
+         if ~isempty(custom_color_map)		% isfield(nii_view, 'color_map')
943 
+            setcolormap = custom_color_map;	% nii_view.color_map;
944 
+         else
945 
+            setcolormap = [];
946 
+         end
947 
+
948 
+         if isfield(nii_view, 'highcolor')
949 
+            sethighcolor = nii_view.highcolor;
950 
+         else
951 
+            sethighcolor = [];
952 
+         end
953 
+
954 
+         redraw_cbar(fig, setcolorlevel, setcolormap, sethighcolor);
955 
+
956 
+         if nii_view.numscan == 1 & ...
957 
+		(custom_colorindex < 2 | custom_colorindex > 3)
958 
+            contrastopt.enablecontrast = 0;
959 
+         else
960 
+            contrastopt.enablecontrast = 1;
961 
+         end
962 
+
963 
+         update_enable(fig, contrastopt);
964 
+
965 
+      end
966 
+
967 
+   case {'neg_color','brightness','contrast'}
968 
+
969 
+      change_colormap(fig);
970 
+
971 
+   case {'brightness_def'}
972 
+
973 
+      nii_view = getappdata(fig,'nii_view');
974 
+      set(nii_view.handles.brightness,'value',0);
975 
+      change_colormap(fig);
976 
+
977 
+   case 'hist_plot'
978 
+
979 
+      hist_plot(fig);
980 
+
981 
+   case 'hist_eq'
982 
+
983 
+      hist_eq(fig);
984 
+
985 
+   case 'move_cursor'
986 
+
987 
+      move_cursor(fig);
988 
+
989 
+   case 'edit_change_scan'
990 
+
991 
+      change_scan('edit_change_scan');
992 
+
993 
+   case 'slider_change_scan'
994 
+
995 
+      change_scan('slider_change_scan');
996 
+
997 
+   end
998 
+
999 
+   return;						% view_nii
1000 
+
1001 
+
1002 
+%----------------------------------------------------------------
1003 
+function fig = init(nii, fig, area, setunit, setviewpoint, setscanid, buttondown, ...
1004 
+         colorindex, color_map, colorlevel, highcolor, cbarminmax, ...
1005 
+         usecolorbar, usepanel, usecrosshair, usestretch, useimagesc, ...
1006 
+         useinterp, setvalue, glblocminmax, setcrosshaircolor, ...
1007 
+         setcomplex)
1008 
+
1009 
+   %  Support data type COMPLEX64 & COMPLEX128
1010 
+   %
1011 
+   if nii.hdr.dime.datatype == 32 | nii.hdr.dime.datatype == 1792
1012 
+      switch setcomplex,
1013 
+      case 0,
1014 
+         nii.img = real(nii.img);
1015 
+      case 1,
1016 
+         nii.img = imag(nii.img);
1017 
+      case 2,
1018 
+         if isa(nii.img, 'double')
1019 
+            nii.img = abs(double(nii.img));
1020 
+         else
1021 
+            nii.img = single(abs(double(nii.img)));
1022 
+         end
1023 
+      end
1024 
+   end
1025 
+
1026 
+   if isempty(area)
1027 
+      area = [0.05 0.05 0.9 0.9];
1028 
+   end
1029 
+
1030 
+   if isempty(setscanid)
1031 
+      setscanid = 1;
1032 
+   else
1033 
+      setscanid = round(setscanid);
1034 
+
1035 
+      if setscanid < 1
1036 
+         setscanid = 1;
1037 
+      end
1038 
+
1039 
+      if setscanid > nii.hdr.dime.dim(5)
1040 
+         setscanid = nii.hdr.dime.dim(5);
1041 
+      end
1042 
+   end
1043 
+
1044 
+   if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
1045 
+      usecolorbar = 0;
1046 
+   elseif isempty(usecolorbar)
1047 
+      usecolorbar = 1;
1048 
+   end
1049 
+
1050 
+   if isempty(usepanel)
1051 
+      usepanel = 1;
1052 
+   end
1053 
+
1054 
+   if isempty(usestretch)
1055 
+      usestretch = 1;
1056 
+   end
1057 
+
1058 
+   if isempty(useimagesc)
1059 
+      useimagesc = 1;
1060 
+   end
1061 
+
1062 
+   if isempty(useinterp)
1063 
+      useinterp = 0;
1064 
+   end
1065 
+
1066 
+   if isempty(colorindex)
1067 
+      tmp = min(nii.img(:,:,:,setscanid));
1068 
+
1069 
+      if  min(tmp(:)) < 0
1070 
+         colorindex = 2;
1071 
+         setcrosshaircolor = [1 1 0];
1072 
+      else
1073 
+         colorindex = 3;
1074 
+      end
1075 
+   end
1076 
+
1077 
+   if isempty(color_map) | ischar(color_map)
1078 
+      color_map = [];
1079 
+   else
1080 
+      colorindex = 1;
1081 
+   end
1082 
+
1083 
+   bgimg = [];
1084 
+
1085 
+   if ~isempty(glblocminmax)
1086 
+      minvalue = glblocminmax(1);
1087 
+      maxvalue = glblocminmax(2);
1088 
+   else
1089 
+      minvalue = double(min(nii.img(:,:,:,setscanid)));
1090 
+      minvalue = min(minvalue(:));
1091 
+      maxvalue = double(max(nii.img(:,:,:,setscanid)));
1092 
+      maxvalue = max(maxvalue(:));
1093 
+   end
1094 
+
1095 
+   if ~isempty(setvalue)
1096 
+      if ~isempty(glblocminmax)
1097 
+         minvalue = glblocminmax(1);
1098 
+         maxvalue = glblocminmax(2);
1099 
+      else
1100 
+         minvalue = double(min(setvalue.val));
1101 
+         maxvalue = double(max(setvalue.val));
1102 
+      end
1103 
+
1104 
+      bgimg = double(nii.img);
1105 
+      minbg = double(min(bgimg(:)));
1106 
+      maxbg = double(max(bgimg(:)));
1107 
+
1108 
+      bgimg = scale_in(bgimg, minbg, maxbg, 54) + 200;	% scale to 202~256 (level 201 is used for highcolor part tolerance)
1109 
+
1110 
+      %  55 level for brain structure (paded 0 for highcolor level 1, i.e. normal level 201, to make 56 highcolor)
1111 
+      %
1112 
+      highcolor = [zeros(1,3);gray(55)];
1113 
+      cbarminmax = [minvalue maxvalue];
1114 
+
1115 
+      if useinterp
1116 
+
1117 
+         %  scale signal data to 1~200
1118 
+         %
1119 
+         nii.img = repmat(nan, size(nii.img));
1120 
+         nii.img(setvalue.idx) = setvalue.val;
1121 
+
1122 
+         %  199 level for source image (map highest color to 199 instead of 200, give 1 level of tolerance)
1123 
+         %
1124 
+         bgimg = single(scale_out(bgimg, cbarminmax(1), cbarminmax(2), 198));
1125 
+      else
1126 
+
1127 
+         bgimg(setvalue.idx) = 0;
1128 
+
1129 
+         %  scale signal data to 1~200
1130 
+         %
1131 
+         nii.img = zeros(size(nii.img));
1132 
+         nii.img(setvalue.idx) = scale_in(setvalue.val, minvalue, maxvalue, 198);
1133 
+         nii.img = nii.img + bgimg;
1134 
+         bgimg = [];
1135 
+         nii.img = scale_out(nii.img, cbarminmax(1), cbarminmax(2), 198);
1136 
+
1137 
+         minvalue = double(min(nii.img(:)));
1138 
+         maxvalue = double(max(nii.img(:)));
1139 
+
1140 
+         if ~isempty(glblocminmax)		% maxvalue is gray
1141 
+            minvalue = glblocminmax(1);
1142 
+         end
1143 
+
1144 
+      end
1145 
+
1146 
+      colorindex = 2;
1147 
+      setcrosshaircolor = [1 1 0];
1148 
+
1149 
+   end
1150 
+
1151 
+   if isempty(highcolor) | ischar(highcolor)
1152 
+      highcolor = [];
1153 
+      num_highcolor = 0;
1154 
+   else
1155 
+      num_highcolor = size(highcolor,1);
1156 
+   end
1157 
+
1158 
+   if isempty(colorlevel)
1159 
+      colorlevel = 256 - num_highcolor;
1160 
+   end
1161 
+
1162 
+   if usecolorbar
1163 
+      cbar_area = area;
1164 
+      cbar_area(1) = area(1) + area(3)*0.93;
1165 
+      cbar_area(3) = area(3)*0.04;
1166 
+      area(3) = area(3)*0.9;		% 90% used for main axes
1167 
+   else
1168 
+      cbar_area = [];
1169 
+   end
1170 
+
1171 
+   %  init color (gray) scaling to make sure the slice clim take the
1172 
+   %  global clim [min(nii.img(:)) max(nii.img(:))]
1173 
+   %
1174 
+   if isempty(bgimg)
1175 
+      clim = [minvalue maxvalue];
1176 
+   else
1177 
+      clim = [minvalue double(max(bgimg(:)))];
1178 
+   end
1179 
+
1180 
+   if clim(1) == clim(2)
1181 
+      clim(2) = clim(1) + 0.000001;
1182 
+   end
1183 
+
1184 
+   if isempty(cbarminmax)
1185 
+      cbarminmax = [minvalue maxvalue];
1186 
+   end
1187 
+
1188 
+   xdim = size(nii.img, 1);
1189 
+   ydim = size(nii.img, 2);
1190 
+   zdim = size(nii.img, 3);
1191 
+
1192 
+   dims = [xdim ydim zdim];
1193 
+   voxel_size = abs(nii.hdr.dime.pixdim(2:4));		% vol in mm
1194 
+
1195 
+   if any(voxel_size <= 0)
1196 
+      voxel_size(find(voxel_size <= 0)) = 1;
1197 
+   end
1198 
+
1199 
+   origin = abs(nii.hdr.hist.originator(1:3));
1200 
+
1201 
+   if isempty(origin) | all(origin == 0)		% according to SPM
1202 
+      origin = (dims+1)/2;
1203 
+   end;
1204 
+
1205 
+   origin = round(origin);
1206 
+
1207 
+   if any(origin > dims)				% simulate fMRI
1208 
+      origin(find(origin > dims)) = dims(find(origin > dims));
1209 
+   end
1210 
+
1211 
+   if any(origin <= 0)
1212 
+      origin(find(origin <= 0)) = 1;
1213 
+   end
1214 
+
1215 
+   nii_view.dims = dims;
1216 
+   nii_view.voxel_size = voxel_size;
1217 
+   nii_view.origin = origin;
1218 
+
1219 
+   nii_view.slices.sag = 1;
1220 
+   nii_view.slices.cor = 1;
1221 
+   nii_view.slices.axi = 1;
1222 
+   if xdim > 1, nii_view.slices.sag = origin(1); end
1223 
+   if ydim > 1, nii_view.slices.cor = origin(2); end
1224 
+   if zdim > 1, nii_view.slices.axi = origin(3); end
1225 
+
1226 
+   nii_view.area = area;
1227 
+   nii_view.fig = fig;
1228 
+   nii_view.nii = nii;					% image data
1229 
+   nii_view.bgimg = bgimg;				% background
1230 
+   nii_view.setvalue = setvalue;
1231 
+   nii_view.minvalue = minvalue;
1232 
+   nii_view.maxvalue = maxvalue;
1233 
+   nii_view.numscan = nii.hdr.dime.dim(5);
1234 
+   nii_view.scanid = setscanid;
1235 
+
1236 
+   Font.FontUnits  = 'point';
1237 
+   Font.FontSize   = 12;
1238 
+
1239 
+   %  create axes for colorbar
1240 
+   %
1241 
+   [cbar_axes cbarminmax_axes] = create_cbar_axes(fig, cbar_area);
1242 
+
1243 
+   if isempty(cbar_area)
1244 
+      nii_view.cbar_area = [];
1245 
+   else
1246 
+      nii_view.cbar_area = cbar_area;
1247 
+   end
1248 
+
1249 
+   %  create axes for top/front/side view
1250 
+   %
1251 
+   vol_size = voxel_size .* dims;
1252 
+   [top_ax, front_ax, side_ax] ...
1253 
+	= create_ax(fig, area, vol_size, usestretch);
1254 
+
1255 
+   top_pos = get(top_ax,'position');
1256 
+   front_pos = get(front_ax,'position');
1257 
+   side_pos = get(side_ax,'position');
1258 
+
1259 
+   %  Sagittal Slider
1260 
+   %
1261 
+   x = side_pos(1);
1262 
+   y = top_pos(2) + top_pos(4);
1263 
+   w = side_pos(3);
1264 
+   h = (front_pos(2) - y) / 2;
1265 
+   y = y + h;
1266 
+
1267 
+   pos = [x y w h];
1268 
+
1269 
+   if xdim > 1,
1270 
+      slider_step(1) = 1/(xdim);
1271 
+      slider_step(2) = 1.00001/(xdim);
1272 
+
1273 
+      handles.sagittal_slider = uicontrol('Parent',fig, ...
1274 
+                'Style','slider','Units','Normalized', Font, ...
1275 
+                'Position',pos, 'HorizontalAlignment','center',...
1276 
+                'BackgroundColor',[0.5 0.5 0.5],'ForegroundColor',[0 0 0],...
1277 
+                'BusyAction','queue',...
1278 
+                'TooltipString','Sagittal slice navigation',...
1279 
+                'Min',1,'Max',xdim,'SliderStep',slider_step, ...
1280 
+                'Value',nii_view.slices.sag,...
1281 
+                'Callback','view_nii(''sagittal_slider'');');
1282 
+
1283 
+      set(handles.sagittal_slider,'position',pos);	% linux66
1284 
+   end
1285 
+
1286 
+   %  Coronal Slider
1287 
+   %
1288 
+   x = top_pos(1);
1289 
+   y = top_pos(2) + top_pos(4);
1290 
+   w = top_pos(3);
1291 
+   h = (front_pos(2) - y) / 2;
1292 
+   y = y + h;
1293 
+
1294 
+   pos = [x y w h];
1295 
+
1296 
+   if ydim > 1,
1297 
+      slider_step(1) = 1/(ydim);
1298 
+      slider_step(2) = 1.00001/(ydim);
1299 
+
1300 
+      slider_val = nii_view.dims(2) - nii_view.slices.cor + 1;
1301 
+
1302 
+      handles.coronal_slider = uicontrol('Parent',fig, ...
1303 
+                'Style','slider','Units','Normalized', Font, ...
1304 
+                'Position',pos, 'HorizontalAlignment','center',...
1305 
+                'BackgroundColor',[0.5 0.5 0.5],'ForegroundColor',[0 0 0],...
1306 
+                'BusyAction','queue',...
1307 
+                'TooltipString','Coronal slice navigation',...
1308 
+                'Min',1,'Max',ydim,'SliderStep',slider_step, ...
1309 
+                'Value',slider_val,...
1310 
+                'Callback','view_nii(''coronal_slider'');');
1311 
+
1312 
+      set(handles.coronal_slider,'position',pos);	% linux66
1313 
+   end
1314 
+
1315 
+   %  Axial Slider
1316 
+   %
1317 
+%   x = front_pos(1) + front_pos(3);
1318 
+%   y = front_pos(2);
1319 
+%   w = side_pos(1) - x;
1320 
+%   h = front_pos(4);
1321 
+
1322 
+   x = top_pos(1);
1323 
+   y = area(2);
1324 
+   w = top_pos(3);
1325 
+   h = top_pos(2) - y;
1326 
+
1327 
+   pos = [x y w h];
1328 
+
1329 
+   if zdim > 1,
1330 
+      slider_step(1) = 1/(zdim);
1331 
+      slider_step(2) = 1.00001/(zdim);
1332 
+
1333 
+      handles.axial_slider = uicontrol('Parent',fig, ...
1334 
+                'Style','slider','Units','Normalized', Font, ...
1335 
+                'Position',pos, 'HorizontalAlignment','center',...
1336 
+                'BackgroundColor',[0.5 0.5 0.5],'ForegroundColor',[0 0 0],...
1337 
+                'BusyAction','queue',...
1338 
+                'TooltipString','Axial slice navigation',...
1339 
+                'Min',1,'Max',zdim,'SliderStep',slider_step, ...
1340 
+                'Value',nii_view.slices.axi,...
1341 
+                'Callback','view_nii(''axial_slider'');');
1342 
+
1343 
+      set(handles.axial_slider,'position',pos);	% linux66
1344 
+   end
1345 
+
1346 
+   %  plot info view
1347 
+   %
1348 
+%   info_pos = [side_pos([1,3]); top_pos([2,4])];
1349 
+%   info_pos = info_pos(:);
1350 
+   gap = side_pos(1)-(top_pos(1)+top_pos(3));
1351 
+   info_pos(1) = side_pos(1) + gap;
1352 
+   info_pos(2) = area(2);
1353 
+   info_pos(3) = side_pos(3) - gap;
1354 
+   info_pos(4) = top_pos(2) + top_pos(4) - area(2) - gap;
1355 
+
1356 
+   num_inputline = 10;
1357 
+   inputline_space =info_pos(4) / num_inputline;
1358 
+
1359 
+
1360 
+   %  for any info_area change, update_usestretch should also be changed
1361 
+
1362 
+
1363 
+   %  Image Intensity Value at Cursor
1364 
+   %
1365 
+   x = info_pos(1);
1366 
+   y = info_pos(2);
1367 
+   w = info_pos(3)*0.5;
1368 
+   h = inputline_space*0.6;
1369 
+
1370 
+   pos = [x y w h];
1371 
+
1372 
+   handles.Timvalcur = uicontrol('Parent',fig,'Style','text', ...
1373 
+      'Units','Normalized', Font, ...
1374 
+      'Position',pos, 'HorizontalAlignment', 'left',...
1375 
+      'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
1376 
+      'BusyAction','queue',...
1377 
+      'visible','off', ...
1378 
+      'String','Value at cursor:');
1379 
+
1380 
+   if usepanel
1381 
+      set(handles.Timvalcur, 'visible', 'on');
1382 
+   end
1383 
+
1384 
+   x = x + w;
1385 
+   w = info_pos(3)*0.5;
1386 
+
1387 
+   pos = [x y w h];
1388 
+
1389 
+   handles.imvalcur = uicontrol('Parent',fig,'Style','text', ...
1390 
+      'Units','Normalized', Font, ...
1391 
+      'Position',pos, 'HorizontalAlignment', 'right',...
1392 
+      'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
1393 
+      'BusyAction','queue',...
1394 
+      'visible','off', ...
1395 
+      'String',' ');
1396 
+
1397 
+   if usepanel
1398 
+      set(handles.imvalcur, 'visible', 'on');
1399 
+   end
1400 
+
1401 
+   %  Position at Cursor
1402 
+   %
1403 
+   x = info_pos(1);
1404 
+   y = y + inputline_space;
1405 
+   w = info_pos(3)*0.5;
1406 
+
1407 
+   pos = [x y w h];
1408 
+
1409 
+   handles.Timposcur = uicontrol('Parent',fig,'Style','text', ...
1410 
+        'Units','Normalized', Font, ...
1411 
+        'Position',pos, 'HorizontalAlignment', 'left',...
1412 
+        'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
1413 
+        'BusyAction','queue',...
1414 
+        'visible','off', ...
1415 
+        'String','[X Y Z] at cursor:');
1416 
+
1417 
+   if usepanel
1418 
+      set(handles.Timposcur, 'visible', 'on');
1419 
+   end
1420 
+
1421 
+   x = x + w;
1422 
+   w = info_pos(3)*0.5;
1423 
+
1424 
+   pos = [x y w h];
1425 
+
1426 
+   handles.imposcur = uicontrol('Parent',fig,'Style','text', ...
1427 
+        'Units','Normalized', Font, ...
1428 
+        'Position',pos, 'HorizontalAlignment', 'right',...
1429 
+        'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
1430 
+        'BusyAction','queue',...
1431 
+        'visible','off', ...
1432 
+        'String',' ','Value',[0 0 0]);
1433 
+
1434 
+   if usepanel
1435 
+      set(handles.imposcur, 'visible', 'on');
1436 
+   end
1437 
+
1438 
+   %  Image Intensity Value at Mouse Click
1439 
+   %
1440 
+   x = info_pos(1);
1441 
+   y = y + inputline_space;
1442 
+   w = info_pos(3)*0.5;
1443 
+
1444 
+   pos = [x y w h];
1445 
+
1446 
+   handles.Timval = uicontrol('Parent',fig,'Style','text', ...
1447 
+      'Units','Normalized', Font, ...
1448 
+      'Position',pos, 'HorizontalAlignment', 'left',...
1449 
+      'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
1450 
+      'BusyAction','queue',...
1451 
+      'visible','off', ...
1452 
+      'String','Value at crosshair:');
1453 
+
1454 
+   if usepanel
1455 
+      set(handles.Timval, 'visible', 'on');
1456 
+   end
1457 
+
1458 
+   x = x + w;
1459 
+   w = info_pos(3)*0.5;
1460 
+
1461 
+   pos = [x y w h];
1462 
+
1463 
+   handles.imval = uicontrol('Parent',fig,'Style','text', ...
1464 
+      'Units','Normalized', Font, ...
1465 
+      'Position',pos, 'HorizontalAlignment', 'right',...
1466 
+      'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
1467 
+      'BusyAction','queue',...
1468 
+      'visible','off', ...
1469 
+      'String',' ');
1470 
+
1471 
+   if usepanel
1472 
+      set(handles.imval, 'visible', 'on');
1473 
+   end
1474 
+
1475 
+   %  Viewpoint Position at Mouse Click
1476 
+   %
1477 
+   x = info_pos(1);
1478 
+   y = y + inputline_space;
1479 
+   w = info_pos(3)*0.5;
1480 
+
1481 
+   pos = [x y w h];
1482 
+
1483 
+   handles.Timpos = uicontrol('Parent',fig,'Style','text', ...
1484 
+        'Units','Normalized', Font, ...
1485 
+        'Position',pos, 'HorizontalAlignment', 'left',...
1486 
+        'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
1487 
+        'BusyAction','queue',...
1488 
+        'visible','off', ...
1489 
+        'String','[X Y Z] at crosshair:');
1490 
+
1491 
+   if usepanel
1492 
+      set(handles.Timpos, 'visible', 'on');
1493 
+   end
1494 
+
1495 
+   x = x + w + 0.005;
1496 
+   y = y - 0.008;
1497 
+   w = info_pos(3)*0.5;
1498 
+   h = inputline_space*0.9;
1499 
+
1500 
+   pos = [x y w h];
1501 
+
1502 
+   handles.impos = uicontrol('Parent',fig,'Style','edit', ...
1503 
+        'Units','Normalized', Font, ...
1504 
+        'Position',pos, 'HorizontalAlignment', 'right',...
1505 
+        'BackgroundColor', [1 1 1], 'ForegroundColor', [0 0 0],...
1506 
+        'BusyAction','queue',...
1507 
+        'Callback','view_nii(''impos_edit'');', ...
1508 
+        'TooltipString','Viewpoint Location in Axes Unit', ...
1509 
+        'visible','off', ...
1510 
+        'String',' ','Value',[0 0 0]);
1511 
+
1512 
+   if usepanel
1513 
+      set(handles.impos, 'visible', 'on');
1514 
+   end
1515 
+
1516 
+   %  Origin Position
1517 
+   %
1518 
+   x = info_pos(1);
1519 
+   y = y + inputline_space*1.2;
1520 
+   w = info_pos(3)*0.5;
1521 
+   h = inputline_space*0.6;
1522 
+
1523 
+   pos = [x y w h];
1524 
+
1525 
+   handles.Torigin = uicontrol('Parent',fig,'Style','text', ...
1526 
+        'Units','Normalized', Font, ...
1527 
+        'Position',pos, 'HorizontalAlignment', 'left',...
1528 
+        'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
1529 
+        'BusyAction','queue',...
1530 
+        'visible','off', ...
1531 
+        'String','[X Y Z] at origin:');
1532 
+
1533 
+   if usepanel
1534 
+      set(handles.Torigin, 'visible', 'on');
1535 
+   end
1536 
+
1537 
+   x = x + w;
1538 
+   w = info_pos(3)*0.5;
1539 
+
1540 
+   pos = [x y w h];
1541 
+
1542 
+   handles.origin = uicontrol('Parent',fig,'Style','text', ...
1543 
+        'Units','Normalized', Font, ...
1544 
+        'Position',pos, 'HorizontalAlignment', 'right',...
1545 
+        'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
1546 
+        'BusyAction','queue',...
1547 
+        'visible','off', ...
1548 
+        'String',' ','Value',[0 0 0]);
1549 
+
1550 
+   if usepanel
1551 
+      set(handles.origin, 'visible', 'on');
1552 
+   end
1553 
+
1554 
+if 0
1555 
+   %  Voxel Unit
1556 
+   %
1557 
+   x = info_pos(1);
1558 
+   y = y + inputline_space;
1559 
+   w = info_pos(3)*0.5;
1560 
+
1561 
+   pos = [x y w h];
1562 
+
1563 
+   handles.Tcoord = uicontrol('Parent',fig,'Style','text', ...
1564 
+      'Units','Normalized', Font, ...
1565 
+      'Position',pos, 'HorizontalAlignment', 'left',...
1566 
+      'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
1567 
+      'BusyAction','queue',...
1568 
+      'visible','off', ...
1569 
+      'String','Axes Unit:');
1570 
+
1571 
+   if usepanel
1572 
+      set(handles.Tcoord, 'visible', 'on');
1573 
+   end
1574 
+
1575 
+   x = x + w + 0.005;
1576 
+   w = info_pos(3)*0.5 - 0.005;
1577 
+
1578 
+   pos = [x y w h];
1579 
+
1580 
+   Font.FontSize   = 8;
1581 
+
1582 
+   handles.coord = uicontrol('Parent',fig,'Style','popupmenu', ...
1583 
+      'Units','Normalized', Font, ...
1584 
+      'Position',pos, ...
1585 
+      'BackgroundColor', [1 1 1], 'ForegroundColor', [0 0 0],...
1586 
+      'BusyAction','queue',...
1587 
+      'TooltipString','Choose Voxel or Millimeter',...
1588 
+      'String',{'Voxel','Millimeter'},...
1589 
+      'visible','off', ...
1590 
+      'Callback','view_nii(''coordinates'');');
1591 
+
1592 
+%      'TooltipString','Choose Voxel, MNI or Talairach Coordinates',...
1593 
+%      'String',{'Voxel','MNI (mm)','Talairach (mm)'},...
1594 
+
1595 
+   Font.FontSize   = 12;
1596 
+
1597 
+   if usepanel
1598 
+      set(handles.coord, 'visible', 'on');
1599 
+   end
1600 
+end
1601 
+
1602 
+   %  Crosshair
1603 
+   %
1604 
+   x = info_pos(1);
1605 
+   y = y + inputline_space;
1606 
+   w = info_pos(3)*0.4;
1607 
+
1608 
+   pos = [x y w h];
1609 
+
1610 
+   handles.Txhair = uicontrol('Parent',fig,'Style','text', ...
1611 
+      'Units','Normalized', Font, ...
1612 
+      'Position',pos, 'HorizontalAlignment', 'left',...
1613 
+      'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
1614 
+      'BusyAction','queue',...
1615 
+      'visible','off', ...
1616 
+      'String','Crosshair:');
1617 
+
1618 
+   if usepanel
1619 
+      set(handles.Txhair, 'visible', 'on');
1620 
+   end
1621 
+
1622 
+   x = info_pos(1) + info_pos(3)*0.5;
1623 
+   w = info_pos(3)*0.2;
1624 
+   h = inputline_space*0.7;
1625 
+
1626 
+   pos = [x y w h];
1627 
+
1628 
+   Font.FontSize   = 8;
1629 
+
1630 
+   handles.xhair_color = uicontrol('Parent',fig,'Style','push', ...
1631 
+      'Units','Normalized', Font, ...
1632 
+      'Position',pos, 'HorizontalAlignment', 'center',...
1633 
+      'TooltipString','Crosshair Color',...
1634 
+      'User',[1 0 0],...
1635 
+      'String','Color',...
1636 
+      'visible','off', ...
1637 
+      'Callback','view_nii(''xhair_color'');');
1638 
+
1639 
+   if usepanel
1640 
+      set(handles.xhair_color, 'visible', 'on');
1641 
+   end
1642 
+
1643 
+   x = info_pos(1) + info_pos(3)*0.7;
1644 
+   w = info_pos(3)*0.3;
1645 
+
1646 
+   pos = [x y w h];
1647 
+
1648 
+   handles.xhair = uicontrol('Parent',fig,'Style','popupmenu', ...
1649 
+      'Units','Normalized', Font, ...
1650 
+      'Position',pos, ...
1651 
+      'BackgroundColor', [1 1 1], 'ForegroundColor', [0 0 0],...
1652 
+      'BusyAction','queue',...
1653 
+      'TooltipString','Display or Hide Crosshair',...
1654 
+      'String',{'On','Off'},...
1655 
+      'visible','off', ...
1656 
+      'Callback','view_nii(''crosshair'');');
1657 
+
1658 
+   if usepanel
1659 
+      set(handles.xhair, 'visible', 'on');
1660 
+   end
1661 
+
1662 
+   %  Histogram & Color
1663 
+   %
1664 
+   x = info_pos(1);
1665 
+   w = info_pos(3)*0.45;
1666 
+   h = inputline_space * 1.5;
1667 
+
1668 
+   pos = [x,  y+inputline_space*0.9,  w,  h];
1669 
+
1670 
+   handles.hist_frame = uicontrol('Parent',fig, ...
1671 
+   	'Units','normal', ...
1672 
+   	'BackgroundColor',[0.8 0.8 0.8], ...
1673 
+   	'Position',pos, ...
1674 
+        'visible','off', ...
1675 
+   	'Style','frame');
1676 
+
1677 
+   if usepanel
1678 
+%      set(handles.hist_frame, 'visible', 'on');
1679 
+   end
1680 
+
1681 
+   handles.coord_frame = uicontrol('Parent',fig, ...
1682 
+   	'Units','normal', ...
1683 
+   	'BackgroundColor',[0.8 0.8 0.8], ...
1684 
+   	'Position',pos, ...
1685 
+        'visible','off', ...
1686 
+   	'Style','frame');
1687 
+
1688 
+   if usepanel
1689 
+      set(handles.coord_frame, 'visible', 'on');
1690 
+   end
1691 
+
1692 
+   x = info_pos(1) + info_pos(3)*0.475;
1693 
+   w = info_pos(3)*0.525;
1694 
+   h = inputline_space * 1.5;
1695 
+
1696 
+   pos = [x,  y+inputline_space*0.9,  w,  h];
1697 
+
1698 
+   handles.color_frame = uicontrol('Parent',fig, ...
1699 
+   	'Units','normal', ...
1700 
+   	'BackgroundColor',[0.8 0.8 0.8], ...
1701 
+   	'Position',pos, ...
1702 
+        'visible','off', ...
1703 
+   	'Style','frame');
1704 
+
1705 
+   if usepanel
1706 
+      set(handles.color_frame, 'visible', 'on');
1707 
+   end
1708 
+
1709 
+   x = info_pos(1) + info_pos(3)*0.025;
1710 
+   y = y + inputline_space*1.2;
1711 
+   w = info_pos(3)*0.2;
1712 
+   h = inputline_space*0.7;
1713 
+
1714 
+   pos = [x y w h];
1715 
+
1716 
+   Font.FontSize   = 8;
1717 
+
1718 
+   handles.hist_eq = uicontrol('Parent',fig,'Style','toggle', ...
1719 
+      'Units','Normalized', Font, ...
1720 
+      'Position',pos, 'HorizontalAlignment', 'center',...
1721 
+      'TooltipString','Histogram Equalization',...
1722 
+      'String','Hist EQ',...
1723 
+      'visible','off', ...
1724 
+      'Callback','view_nii(''hist_eq'');');
1725 
+
1726 
+   if usepanel
1727 
+%      set(handles.hist_eq, 'visible', 'on');
1728 
+   end
1729 
+
1730 
+   x = x + w;
1731 
+   w = info_pos(3)*0.2;
1732 
+
1733 
+   pos = [x y w h];
1734 
+
1735 
+   handles.hist_plot = uicontrol('Parent',fig,'Style','push', ...
1736 
+      'Units','Normalized', Font, ...
1737 
+      'Position',pos, 'HorizontalAlignment', 'center',...
1738 
+      'TooltipString','Histogram Plot',...
1739 
+      'String','Hist Plot',...
1740 
+      'visible','off', ...
1741 
+      'Callback','view_nii(''hist_plot'');');
1742 
+
1743 
+   if usepanel
1744 
+%      set(handles.hist_plot, 'visible', 'on');
1745 
+   end
1746 
+
1747 
+   x = info_pos(1) + info_pos(3)*0.025;
1748 
+   w = info_pos(3)*0.4;
1749 
+
1750 
+   pos = [x y w h];
1751 
+
1752 
+   handles.coord = uicontrol('Parent',fig,'Style','popupmenu', ...
1753 
+      'Units','Normalized', Font, ...
1754 
+      'Position',pos, ...
1755 
+      'BackgroundColor', [1 1 1], 'ForegroundColor', [0 0 0],...
1756 
+      'BusyAction','queue',...
1757 
+      'TooltipString','Choose Voxel or Millimeter',...
1758 
+      'String',{'Voxel','Millimeter'},...
1759 
+      'visible','off', ...
1760 
+      'Callback','view_nii(''coordinates'');');
1761 
+
1762 
+%      'TooltipString','Choose Voxel, MNI or Talairach Coordinates',...
1763 
+%      'String',{'Voxel','MNI (mm)','Talairach (mm)'},...
1764 
+
1765 
+   if usepanel
1766 
+      set(handles.coord, 'visible', 'on');
1767 
+   end
1768 
+
1769 
+   x = info_pos(1) + info_pos(3)*0.5;
1770 
+   w = info_pos(3)*0.2;
1771 
+
1772 
+   pos = [x y w h];
1773 
+
1774 
+   handles.neg_color = uicontrol('Parent',fig,'Style','toggle', ...
1775 
+      'Units','Normalized', Font, ...
1776 
+      'Position',pos, 'HorizontalAlignment', 'center',...
1777 
+      'TooltipString','Negative Colormap',...
1778 
+      'String','Negative',...
1779 
+      'visible','off', ...
1780 
+      'Callback','view_nii(''neg_color'');');
1781 
+
1782 
+   if usepanel
1783 
+      set(handles.neg_color, 'visible', 'on');
1784 
+   end
1785 
+
1786 
+   if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
1787 
+      set(handles.neg_color, 'enable', 'off');
1788 
+   end
1789 
+
1790 
+   x = info_pos(1) + info_pos(3)*0.7;
1791 
+   w = info_pos(3)*0.275;
1792 
+
1793 
+   pos = [x y w h];
1794 
+
1795 
+   handles.colorindex = uicontrol('Parent',fig,'Style','popupmenu', ...
1796 
+      'Units','Normalized', Font, ...
1797 
+      'Position',pos, ...
1798 
+      'BackgroundColor', [1 1 1], 'ForegroundColor', [0 0 0],...
1799 
+      'BusyAction','queue',...
1800 
+      'TooltipString','Change Colormap',...
1801 
+      'String',{'Custom','Bipolar','Gray','Jet','Cool','Bone','Hot','Copper','Pink'},...
1802 
+      'value', colorindex, ...
1803 
+      'visible','off', ...
1804 
+      'Callback','view_nii(''color'');');
1805 
+
1806 
+   if usepanel
1807 
+      set(handles.colorindex, 'visible', 'on');
1808 
+   end
1809 
+
1810 
+   if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
1811 
+      set(handles.colorindex, 'enable', 'off');
1812 
+   end
1813 
+
1814 
+   x = info_pos(1) + info_pos(3)*0.1;
1815 
+   y = y + inputline_space;
1816 
+   w = info_pos(3)*0.28;
1817 
+   h = inputline_space*0.6;
1818 
+
1819 
+   pos = [x y w h];
1820 
+
1821 
+   Font.FontSize   = 8;
1822 
+
1823 
+   handles.Thist = uicontrol('Parent',fig,'Style','text', ...
1824 
+      'Units','Normalized', Font, ...
1825 
+      'Position',pos, 'HorizontalAlignment', 'center',...
1826 
+      'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
1827 
+      'BusyAction','queue',...
1828 
+      'visible','off', ...
1829 
+      'String','Histogram');
1830 
+
1831 
+   handles.Tcoord = uicontrol('Parent',fig,'Style','text', ...
1832 
+      'Units','Normalized', Font, ...
1833 
+      'Position',pos, 'HorizontalAlignment', 'center',...
1834 
+      'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
1835 
+      'BusyAction','queue',...
1836 
+      'visible','off', ...
1837 
+      'String','Axes Unit');
1838 
+
1839 
+   if usepanel
1840 
+%      set(handles.Thist, 'visible', 'on');
1841 
+      set(handles.Tcoord, 'visible', 'on');
1842 
+   end
1843 
+
1844 
+   x = info_pos(1) + info_pos(3)*0.60;
1845 
+   w = info_pos(3)*0.28;
1846 
+
1847 
+   pos = [x y w h];
1848 
+
1849 
+   handles.Tcolor = uicontrol('Parent',fig,'Style','text', ...
1850 
+      'Units','Normalized', Font, ...
1851 
+      'Position',pos, 'HorizontalAlignment', 'center',...
1852 
+      'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
1853 
+      'BusyAction','queue',...
1854 
+      'visible','off', ...
1855 
+      'String','Colormap');
1856 
+
1857 
+   if usepanel
1858 
+      set(handles.Tcolor, 'visible', 'on');
1859 
+   end
1860 
+
1861 
+   if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
1862 
+      set(handles.Tcolor, 'enable', 'off');
1863 
+   end
1864 
+
1865 
+   %  Contrast Frame
1866 
+   %
1867 
+   x = info_pos(1);
1868 
+   w = info_pos(3)*0.45;
1869 
+   h = inputline_space * 2;
1870 
+
1871 
+   pos = [x,  y+inputline_space*0.8,  w,  h];
1872 
+
1873 
+   handles.contrast_frame = uicontrol('Parent',fig, ...
1874 
+   	'Units','normal', ...
1875 
+   	'BackgroundColor',[0.8 0.8 0.8], ...
1876 
+   	'Position',pos, ...
1877 
+        'visible','off', ...
1878 
+   	'Style','frame');
1879 
+
1880 
+   if usepanel
1881 
+      set(handles.contrast_frame, 'visible', 'on');
1882 
+   end
1883 
+
1884 
+   if colorindex < 2 | colorindex > 3
1885 
+      set(handles.contrast_frame, 'visible', 'off');
1886 
+   end
1887 
+
1888 
+   %  Brightness Frame
1889 
+   %
1890 
+   x = info_pos(1) + info_pos(3)*0.475;
1891 
+   w = info_pos(3)*0.525;
1892 
+
1893 
+   pos = [x,  y+inputline_space*0.8,  w,  h];
1894 
+
1895 
+   handles.brightness_frame = uicontrol('Parent',fig, ...
1896 
+   	'Units','normal', ...
1897 
+   	'BackgroundColor',[0.8 0.8 0.8], ...
1898 
+   	'Position',pos, ...
1899 
+        'visible','off', ...
1900 
+   	'Style','frame');
1901 
+
1902 
+   if usepanel
1903 
+      set(handles.brightness_frame, 'visible', 'on');
1904 
+   end
1905 
+
1906 
+   %  Contrast
1907 
+   %
1908 
+   x = info_pos(1) + info_pos(3)*0.025;
1909 
+   y = y + inputline_space;
1910 
+   w = info_pos(3)*0.4;
1911 
+   h = inputline_space*0.6;
1912 
+
1913 
+   pos = [x y w h];
1914 
+
1915 
+   Font.FontSize   = 12;
1916 
+
1917 
+   slider_step(1) = 5/255;
1918 
+   slider_step(2) = 5.00001/255;
1919 
+
1920 
+   handles.contrast = uicontrol('Parent',fig, ...
1921 
+      'Style','slider','Units','Normalized', Font, ...
1922 
+      'Position',pos, 'HorizontalAlignment', 'left',...
1923 
+      'BackgroundColor',[0.5 0.5 0.5],'ForegroundColor',[0 0 0],...
1924 
+      'BusyAction','queue',...
1925 
+      'TooltipString','Change contrast',...
1926 
+      'Min',1,'Max',256,'SliderStep',slider_step, ...
1927 
+      'Value',1, ...
1928 
+      'visible','off', ...
1929 
+      'Callback','view_nii(''contrast'');');
1930 
+
1931 
+   if usepanel
1932 
+      set(handles.contrast, 'visible', 'on');
1933 
+   end
1934 
+
1935 
+   if (nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511) & nii_view.numscan <= 1
1936 
+      set(handles.contrast, 'enable', 'off');
1937 
+   end
1938 
+
1939 
+   if nii_view.numscan > 1
1940 
+      set(handles.contrast, 'min', 1, 'max', nii_view.numscan, ...
1941 
+         'sliderstep',[1/(nii_view.numscan-1) 1.00001/(nii_view.numscan-1)], ...
1942 
+         'Callback', 'view_nii(''slider_change_scan'');');
1943 
+   elseif colorindex < 2 | colorindex > 3
1944 
+      set(handles.contrast, 'visible', 'off');
1945 
+   elseif colorindex == 2
1946 
+      set(handles.contrast,'value',128);
1947 
+   end
1948 
+
1949 
+   set(handles.contrast,'position',pos);	% linux66
1950 
+
1951 
+   %  Brightness
1952 
+   %
1953 
+   x = info_pos(1) + info_pos(3)*0.5;
1954 
+   w = info_pos(3)*0.475;
1955 
+
1956 
+   pos = [x y w h];
1957 
+
1958 
+   Font.FontSize   = 12;
1959 
+
1960 
+   slider_step(1) = 1/50;
1961 
+   slider_step(2) = 1.00001/50;
1962 
+
1963 
+   handles.brightness = uicontrol('Parent',fig, ...
1964 
+      'Style','slider','Units','Normalized', Font, ...
1965 
+      'Position',pos, 'HorizontalAlignment', 'left',...
1966 
+      'BackgroundColor',[0.5 0.5 0.5],'ForegroundColor',[0 0 0],...
1967 
+      'BusyAction','queue',...
1968 
+      'TooltipString','Change brightness',...
1969 
+      'Min',-1,'Max',1,'SliderStep',slider_step, ...
1970 
+      'Value',0, ...
1971 
+      'visible','off', ...
1972 
+      'Callback','view_nii(''brightness'');');
1973 
+
1974 
+   if usepanel
1975 
+      set(handles.brightness, 'visible', 'on');
1976 
+   end
1977 
+
1978 
+   if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
1979 
+      set(handles.brightness, 'enable', 'off');
1980 
+   end
1981 
+
1982 
+   set(handles.brightness,'position',pos);	% linux66
1983 
+
1984 
+   %  Contrast text/def
1985 
+   %
1986 
+   x = info_pos(1) + info_pos(3)*0.025;
1987 
+   y = y + inputline_space;
1988 
+   w = info_pos(3)*0.22;
1989 
+
1990 
+   pos = [x y w h];
1991 
+
1992 
+   handles.Tcontrast = uicontrol('Parent',fig,'Style','text', ...
1993 
+      'Units','Normalized', Font, ...
1994 
+      'Position',pos, 'HorizontalAlignment', 'left',...
1995 
+      'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
1996 
+      'BusyAction','queue',...
1997 
+      'visible','off', ...
1998 
+      'String','Contrast:');
1999 
+
2000 
+   if usepanel
2001 
+      set(handles.Tcontrast, 'visible', 'on');
2002 
+   end
2003 
+
2004 
+   if (nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511) & nii_view.numscan <= 1
2005 
+      set(handles.Tcontrast, 'enable', 'off');
2006 
+   end
2007 
+
2008 
+   if nii_view.numscan > 1
2009 
+      set(handles.Tcontrast, 'string', 'Scan ID:');
2010 
+   elseif colorindex < 2 | colorindex > 3
2011 
+      set(handles.Tcontrast, 'visible', 'off');
2012 
+   end
2013 
+
2014 
+   x = x + w;
2015 
+   w = info_pos(3)*0.18;
2016 
+
2017 
+   pos = [x y w h];
2018 
+
2019 
+   Font.FontSize   = 8;
2020 
+
2021 
+   handles.contrast_def = uicontrol('Parent',fig,'Style','push', ...
2022 
+      'Units','Normalized', Font, ...
2023 
+      'Position',pos, 'HorizontalAlignment', 'center',...
2024 
+      'TooltipString','Restore initial contrast',...
2025 
+      'String','Reset',...
2026 
+      'visible','off', ...
2027 
+      'Callback','view_nii(''contrast_def'');');
2028 
+
2029 
+   if usepanel
2030 
+      set(handles.contrast_def, 'visible', 'on');
2031 
+   end
2032 
+
2033 
+   if (nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511) & nii_view.numscan <= 1
2034 
+      set(handles.contrast_def, 'enable', 'off');
2035 
+   end
2036 
+
2037 
+   if nii_view.numscan > 1
2038 
+      set(handles.contrast_def, 'style', 'edit', 'background', 'w', ...
2039 
+         'TooltipString','Scan (or volume) index in the time series',...
2040 
+         'string', '1', 'Callback', 'view_nii(''edit_change_scan'');');
2041 
+   elseif colorindex < 2 | colorindex > 3
2042 
+      set(handles.contrast_def, 'visible', 'off');
2043 
+   end
2044 
+
2045 
+   %  Brightness text/def
2046 
+   %
2047 
+   x = info_pos(1) + info_pos(3)*0.5;
2048 
+   w = info_pos(3)*0.295;
2049 
+
2050 
+   pos = [x y w h];
2051 
+
2052 
+   Font.FontSize   = 12;
2053 
+
2054 
+   handles.Tbrightness = uicontrol('Parent',fig,'Style','text', ...
2055 
+      'Units','Normalized', Font, ...
2056 
+      'Position',pos, 'HorizontalAlignment', 'left',...
2057 
+      'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
2058 
+      'BusyAction','queue',...
2059 
+      'visible','off', ...
2060 
+      'String','Brightness:');
2061 
+
2062 
+   if usepanel
2063 
+      set(handles.Tbrightness, 'visible', 'on');
2064 
+   end
2065 
+
2066 
+   if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
2067 
+      set(handles.Tbrightness, 'enable', 'off');
2068 
+   end
2069 
+
2070 
+   x = x + w;
2071 
+   w = info_pos(3)*0.18;
2072 
+
2073 
+   pos = [x y w h];
2074 
+
2075 
+   Font.FontSize   = 8;
2076 
+
2077 
+   handles.brightness_def = uicontrol('Parent',fig,'Style','push', ...
2078 
+      'Units','Normalized', Font, ...
2079 
+      'Position',pos, 'HorizontalAlignment', 'center',...
2080 
+      'TooltipString','Restore initial brightness',...
2081 
+      'String','Reset',...
2082 
+      'visible','off', ...
2083 
+      'Callback','view_nii(''brightness_def'');');
2084 
+
2085 
+   if usepanel
2086 
+      set(handles.brightness_def, 'visible', 'on');
2087 
+   end
2088 
+
2089 
+   if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
2090 
+      set(handles.brightness_def, 'enable', 'off');
2091 
+   end
2092 
+
2093 
+   %  init image handles
2094 
+   %
2095 
+   handles.axial_image = [];
2096 
+   handles.coronal_image = [];
2097 
+   handles.sagittal_image = [];
2098 
+
2099 
+   %  plot axial view
2100 
+   %
2101 
+   if ~isempty(nii_view.bgimg)
2102 
+      bg_slice = squeeze(bgimg(:,:,nii_view.slices.axi));
2103 
+      h1 = plot_view(fig, xdim, ydim, top_ax, bg_slice', clim, cbarminmax, ...
2104 
+		handles, useimagesc, colorindex, color_map, ...
2105 
+		colorlevel, highcolor, useinterp, nii_view.numscan);
2106 
+      handles.axial_bg = h1;
2107 
+   else
2108 
+      handles.axial_bg = [];
2109 
+   end
2110 
+
2111 
+   if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
2112 
+      img_slice = squeeze(nii.img(:,:,nii_view.slices.axi,:,setscanid));
2113 
+      img_slice = permute(img_slice, [2 1 3]);
2114 
+   else
2115 
+      img_slice = squeeze(nii.img(:,:,nii_view.slices.axi,setscanid));
2116 
+      img_slice = img_slice';
2117 
+   end
2118 
+   h1 = plot_view(fig, xdim, ydim, top_ax, img_slice, clim, cbarminmax, ...
2119 
+	handles, useimagesc, colorindex, color_map, ...
2120 
+	colorlevel, highcolor, useinterp, nii_view.numscan);
2121 
+   set(h1,'buttondown','view_nii(''axial_image'');');
2122 
+   handles.axial_image = h1;
2123 
+   handles.axial_axes = top_ax;
2124 
+
2125 
+   if size(img_slice,1) == 1 | size(img_slice,2) == 1
2126 
+      set(top_ax,'visible','off');
2127 
+
2128 
+      if isfield(handles,'sagittal_slider') & ishandle(handles.sagittal_slider)
2129 
+         set(handles.sagittal_slider, 'visible', 'off');
2130 
+      end
2131 
+
2132 
+      if isfield(handles,'coronal_slider') & ishandle(handles.coronal_slider)
2133 
+         set(handles.coronal_slider, 'visible', 'off');
2134 
+      end
2135 
+
2136 
+      if isfield(handles,'axial_slider') & ishandle(handles.axial_slider)
2137 
+         set(handles.axial_slider, 'visible', 'off');
2138 
+      end
2139 
+   end
2140 
+
2141 
+   %  plot coronal view
2142 
+   %
2143 
+   if ~isempty(nii_view.bgimg)
2144 
+      bg_slice = squeeze(bgimg(:,nii_view.slices.cor,:));
2145 
+      h1 = plot_view(fig, xdim, zdim, front_ax, bg_slice', clim, cbarminmax, ...
2146 
+		handles, useimagesc, colorindex, color_map, ...
2147 
+		colorlevel, highcolor, useinterp, nii_view.numscan);
2148 
+      handles.coronal_bg = h1;
2149 
+   else
2150 
+      handles.coronal_bg = [];
2151 
+   end
2152 
+
2153 
+   if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
2154 
+      img_slice = squeeze(nii.img(:,nii_view.slices.cor,:,:,setscanid));
2155 
+      img_slice = permute(img_slice, [2 1 3]);
2156 
+   else
2157 
+      img_slice = squeeze(nii.img(:,nii_view.slices.cor,:,setscanid));
2158 
+      img_slice = img_slice';
2159 
+   end
2160 
+   h1 = plot_view(fig, xdim, zdim, front_ax, img_slice, clim, cbarminmax, ...
2161 
+	handles, useimagesc, colorindex, color_map, ...
2162 
+	colorlevel, highcolor, useinterp, nii_view.numscan);
2163 
+   set(h1,'buttondown','view_nii(''coronal_image'');');
2164 
+   handles.coronal_image = h1;
2165 
+   handles.coronal_axes = front_ax;
2166 
+
2167 
+   if size(img_slice,1) == 1 | size(img_slice,2) == 1
2168 
+      set(front_ax,'visible','off');
2169 
+
2170 
+      if isfield(handles,'sagittal_slider') & ishandle(handles.sagittal_slider)
2171 
+         set(handles.sagittal_slider, 'visible', 'off');
2172 
+      end
2173 
+
2174 
+      if isfield(handles,'coronal_slider') & ishandle(handles.coronal_slider)
2175 
+         set(handles.coronal_slider, 'visible', 'off');
2176 
+      end
2177 
+
2178 
+      if isfield(handles,'axial_slider') & ishandle(handles.axial_slider)
2179 
+         set(handles.axial_slider, 'visible', 'off');
2180 
+      end
2181 
+   end
2182 
+
2183 
+   %  plot sagittal view
2184 
+   %
2185 
+   if ~isempty(nii_view.bgimg)
2186 
+      bg_slice = squeeze(bgimg(nii_view.slices.sag,:,:));
2187 
+
2188 
+      h1 = plot_view(fig, ydim, zdim, side_ax, bg_slice', clim, cbarminmax, ...
2189 
+		handles, useimagesc, colorindex, color_map, ...
2190 
+		colorlevel, highcolor, useinterp, nii_view.numscan);
2191 
+      handles.sagittal_bg = h1;
2192 
+   else
2193 
+      handles.sagittal_bg = [];
2194 
+   end
2195 
+
2196 
+   if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
2197 
+      img_slice = squeeze(nii.img(nii_view.slices.sag,:,:,:,setscanid));
2198 
+      img_slice = permute(img_slice, [2 1 3]);
2199 
+   else
2200 
+      img_slice = squeeze(nii.img(nii_view.slices.sag,:,:,setscanid));
2201 
+      img_slice = img_slice';
2202 
+   end
2203 
+
2204 
+   h1 = plot_view(fig, ydim, zdim, side_ax, img_slice, clim, cbarminmax, ...
2205 
+	handles, useimagesc, colorindex, color_map, ...
2206 
+	colorlevel, highcolor, useinterp, nii_view.numscan);
2207 
+   set(h1,'buttondown','view_nii(''sagittal_image'');');
2208 
+   set(side_ax,'Xdir', 'reverse');
2209 
+   handles.sagittal_image = h1;
2210 
+   handles.sagittal_axes = side_ax;
2211 
+
2212 
+   if size(img_slice,1) == 1 | size(img_slice,2) == 1
2213 
+      set(side_ax,'visible','off');
2214 
+
2215 
+      if isfield(handles,'sagittal_slider') & ishandle(handles.sagittal_slider)
2216 
+         set(handles.sagittal_slider, 'visible', 'off');
2217 
+      end
2218 
+
2219 
+      if isfield(handles,'coronal_slider') & ishandle(handles.coronal_slider)
2220 
+         set(handles.coronal_slider, 'visible', 'off');
2221 
+      end
2222 
+
2223 
+      if isfield(handles,'axial_slider') & ishandle(handles.axial_slider)
2224 
+         set(handles.axial_slider, 'visible', 'off');
2225 
+      end
2226 
+   end
2227 
+
2228 
+   [top1_label, top2_label, side1_label, side2_label] = ...
2229 
+	dir_label(fig, top_ax, front_ax, side_ax);
2230 
+
2231 
+   %  store label handles
2232 
+   %
2233 
+   handles.top1_label = top1_label;
2234 
+   handles.top2_label = top2_label;
2235 
+   handles.side1_label = side1_label;
2236 
+   handles.side2_label = side2_label;
2237 
+
2238 
+   %  plot colorbar
2239 
+   %
2240 
+   if ~isempty(cbar_axes) & ~isempty(cbarminmax_axes)
2241 
+
2242 
+if 0
2243 
+      if isempty(color_map)
2244 
+         level = colorlevel + num_highcolor;
2245 
+      else
2246 
+         level = size([color_map; highcolor], 1);
2247 
+      end
2248 
+end
2249 
+
2250 
+      if isempty(color_map)
2251 
+         level = colorlevel;
2252 
+      else
2253 
+         level = size([color_map], 1);
2254 
+      end
2255 
+
2256 
+      niiclass = class(nii.img);
2257 
+
2258 
+      h1 = plot_cbar(fig, cbar_axes, cbarminmax_axes, cbarminmax, ...
2259 
+		level, handles, useimagesc, colorindex, color_map, ...
2260 
+		colorlevel, highcolor, niiclass, nii_view.numscan);
2261 
+      handles.cbar_image = h1;
2262 
+      handles.cbar_axes = cbar_axes;
2263 
+      handles.cbarminmax_axes = cbarminmax_axes;
2264 
+
2265 
+   end
2266 
+
2267 
+   nii_view.handles = handles;		% store handles
2268 
+
2269 
+   nii_view.usepanel = usepanel;		% whole panel at low right cornor
2270 
+   nii_view.usestretch = usestretch;	% stretch display of voxel_size
2271 
+   nii_view.useinterp = useinterp;	% use interpolation
2272 
+   nii_view.colorindex = colorindex;	% store colorindex variable
2273 
+   nii_view.buttondown = buttondown;	% command after button down click
2274 
+   nii_view.cbarminmax = cbarminmax;	% store min max value for colorbar
2275 
+
2276 
+   set_coordinates(nii_view,useinterp);	% coord unit
2277 
+
2278 
+   if ~isfield(nii_view, 'axi_xhair') |  ...
2279 
+      ~isfield(nii_view, 'cor_xhair') |  ...
2280 
+      ~isfield(nii_view, 'sag_xhair')
2281 
+
2282 
+      nii_view.axi_xhair = [];			% top cross hair
2283 
+      nii_view.cor_xhair = [];			% front cross hair
2284 
+      nii_view.sag_xhair = [];			% side cross hair
2285 
+
2286 
+   end
2287 
+
2288 
+   if ~isempty(color_map)
2289 
+      nii_view.color_map = color_map;
2290 
+   end
2291 
+
2292 
+   if ~isempty(colorlevel)
2293 
+      nii_view.colorlevel = colorlevel;
2294 
+   end
2295 
+
2296 
+   if ~isempty(highcolor)
2297 
+      nii_view.highcolor = highcolor;
2298 
+   end
2299 
+
2300 
+   update_nii_view(nii_view);
2301 
+
2302 
+   if ~isempty(setunit)
2303 
+      update_unit(fig, setunit);
2304 
+   end
2305 
+
2306 
+   if ~isempty(setviewpoint)
2307 
+      update_viewpoint(fig, setviewpoint);
2308 
+   end
2309 
+
2310 
+   if ~isempty(setcrosshaircolor)
2311 
+      update_crosshaircolor(fig, setcrosshaircolor);
2312 
+   end
2313 
+
2314 
+   if ~isempty(usecrosshair)
2315 
+      update_usecrosshair(fig, usecrosshair);
2316 
+   end
2317 
+
2318 
+   nii_menu = getappdata(fig, 'nii_menu');
2319 
+
2320 
+   if ~isempty(nii_menu)
2321 
+      if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
2322 
+         set(nii_menu.Minterp,'Userdata',1,'Label','Interp on','enable','off');
2323 
+      elseif useinterp
2324 
+         set(nii_menu.Minterp,'Userdata',0,'Label','Interp off');
2325 
+      else
2326 
+         set(nii_menu.Minterp,'Userdata',1,'Label','Interp on');
2327 
+      end
2328 
+   end
2329 
+
2330 
+   windowbuttonmotion = get(fig, 'windowbuttonmotion');
2331 
+   windowbuttonmotion = [windowbuttonmotion '; view_nii(''move_cursor'');'];
2332 
+   set(fig, 'windowbuttonmotion', windowbuttonmotion);
2333 
+
2334 
+   return;						% init
2335 
+
2336 
+
2337 
+%----------------------------------------------------------------
2338 
+function fig = update_img(img, fig, opt)
2339 
+
2340 
+   nii_menu = getappdata(fig,'nii_menu');
2341 
+
2342 
+   if ~isempty(nii_menu)
2343 
+      set(nii_menu.Mzoom,'Userdata',1,'Label','Zoom on');
2344 
+      set(fig,'pointer','arrow');
2345 
+      zoom off;
2346 
+   end
2347 
+
2348 
+   nii_view = getappdata(fig,'nii_view');
2349 
+   change_interp = 0;
2350 
+
2351 
+   if isfield(opt, 'useinterp') & opt.useinterp ~= nii_view.useinterp
2352 
+      nii_view.useinterp = opt.useinterp;
2353 
+      change_interp = 1;
2354 
+   end
2355 
+
2356 
+   setscanid = 1;
2357 
+
2358 
+   if isfield(opt, 'setscanid')
2359 
+      setscanid = round(opt.setscanid);
2360 
+
2361 
+      if setscanid < 1
2362 
+         setscanid = 1;
2363 
+      end
2364 
+
2365 
+      if setscanid > nii_view.numscan
2366 
+         setscanid = nii_view.numscan;
2367 
+      end
2368 
+   end
2369 
+
2370 
+   if isfield(opt, 'glblocminmax') & ~isempty(opt.glblocminmax)
2371 
+      minvalue = opt.glblocminmax(1);
2372 
+      maxvalue = opt.glblocminmax(2);
2373 
+   else
2374 
+      minvalue = double(min(img(:,:,:,setscanid)));
2375 
+      minvalue = min(minvalue(:));
2376 
+      maxvalue = double(max(img(:,:,:,setscanid)));
2377 
+      maxvalue = max(maxvalue(:));
2378 
+   end
2379 
+
2380 
+   if isfield(opt, 'setvalue')
2381 
+      setvalue = opt.setvalue;
2382 
+
2383 
+      if isfield(opt, 'glblocminmax') & ~isempty(opt.glblocminmax)
2384 
+         minvalue = opt.glblocminmax(1);
2385 
+         maxvalue = opt.glblocminmax(2);
2386 
+      else
2387 
+         minvalue = double(min(setvalue.val));
2388 
+         maxvalue = double(max(setvalue.val));
2389 
+      end
2390 
+
2391 
+      bgimg = img;
2392 
+      minbg = min(bgimg(:));
2393 
+      maxbg = max(bgimg(:));
2394 
+      bgimg = scale_in(bgimg, minbg, maxbg, 54) + 200;	% scale to 202~256 (201 is used for highcolor part tolerance)
2395 
+
2396 
+      cbarminmax = [minvalue maxvalue];
2397 
+
2398 
+      if nii_view.useinterp
2399 
+
2400 
+         %  scale signal data to 1~200
2401 
+         %
2402 
+         img = repmat(nan, size(img));
2403 
+         img(setvalue.idx) = setvalue.val;
2404 
+
2405 
+         %  199 level for source image (map highest color to 199 instead of 200, give 1 level of tolerance)
2406 
+         %
2407 
+         bgimg = single(scale_out(bgimg, cbarminmax(1), cbarminmax(2), 198));
2408 
+
2409 
+      else
2410 
+
2411 
+         bgimg(setvalue.idx) = 0;
2412 
+
2413 
+         %  scale signal data to 1~200
2414 
+         %
2415 
+         img = zeros(size(img));
2416 
+         img(setvalue.idx) = scale_in(setvalue.val, minvalue, maxvalue, 198);
2417 
+         img = img + bgimg;
2418 
+         bgimg = [];
2419 
+         img = scale_out(img, cbarminmax(1), cbarminmax(2), 198);
2420 
+
2421 
+         minvalue = double(min(img(:)));
2422 
+         maxvalue = double(max(img(:)));
2423 
+
2424 
+         if isfield(opt,'glblocminmax') & ~isempty(opt.glblocminmax)
2425 
+            minvalue = opt.glblocminmax(1);
2426 
+         end
2427 
+
2428 
+      end
2429 
+
2430 
+      nii_view.bgimg = bgimg;
2431 
+      nii_view.setvalue = setvalue;
2432 
+   else
2433 
+      cbarminmax = [minvalue maxvalue];
2434 
+   end
2435 
+
2436 
+   update_cbarminmax(fig, cbarminmax);
2437 
+   nii_view.cbarminmax = cbarminmax;
2438 
+   nii_view.nii.img = img;
2439 
+   nii_view.minvalue = minvalue;
2440 
+   nii_view.maxvalue = maxvalue;
2441 
+   nii_view.scanid = setscanid;
2442 
+   change_colormap(fig);
2443 
+
2444 
+   %  init color (gray) scaling to make sure the slice clim take the
2445 
+   %  global clim [min(nii.img(:)) max(nii.img(:))]
2446 
+   %
2447 
+   if isempty(nii_view.bgimg)
2448 
+      clim = [minvalue maxvalue];
2449 
+   else
2450 
+      clim = [minvalue double(max(nii_view.bgimg(:)))];
2451 
+   end
2452 
+
2453 
+   if clim(1) == clim(2)
2454 
+      clim(2) = clim(1) + 0.000001;
2455 
+   end
2456 
+
2457 
+   if strcmpi(get(nii_view.handles.axial_image,'cdatamapping'), 'direct')
2458 
+      useimagesc = 0;
2459 
+   else
2460 
+      useimagesc = 1;
2461 
+   end
2462 
+
2463 
+   if ~isempty(nii_view.bgimg)			% with interpolation
2464 
+
2465 
+      Saxi = squeeze(nii_view.bgimg(:,:,nii_view.slices.axi));
2466 
+
2467 
+      if isfield(nii_view.handles,'axial_bg') & ~isempty(nii_view.handles.axial_bg)
2468 
+         set(nii_view.handles.axial_bg,'CData',Saxi');
2469 
+      else
2470 
+         axes(nii_view.handles.axial_axes);
2471 
+
2472 
+         if useimagesc
2473 
+            nii_view.handles.axial_bg = surface(zeros(size(Saxi')),double(Saxi'),'edgecolor','none','facecolor','interp');
2474 
+         else
2475 
+            nii_view.handles.axial_bg = surface(zeros(size(Saxi')),double(Saxi'),'cdatamapping','direct','edgecolor','none','facecolor','interp');
2476 
+         end
2477 
+
2478 
+         order = get(gca,'child');
2479 
+         order(find(order == nii_view.handles.axial_bg)) = [];
2480 
+         order = [order; nii_view.handles.axial_bg];
2481 
+         set(gca, 'child', order);
2482 
+      end
2483 
+
2484 
+   end
2485 
+
2486 
+   if isfield(nii_view.handles,'axial_image'),
2487 
+      if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
2488 
+         Saxi = squeeze(nii_view.nii.img(:,:,nii_view.slices.axi,:,setscanid));
2489 
+         Saxi = permute(Saxi, [2 1 3]);
2490 
+      else
2491 
+         Saxi = squeeze(nii_view.nii.img(:,:,nii_view.slices.axi,setscanid));
2492 
+         Saxi = Saxi';
2493 
+      end
2494 
+
2495 
+      set(nii_view.handles.axial_image,'CData',Saxi);
2496 
+   end
2497 
+
2498 
+   set(nii_view.handles.axial_axes,'CLim',clim);
2499 
+
2500 
+   if ~isempty(nii_view.bgimg)
2501 
+      Scor = squeeze(nii_view.bgimg(:,nii_view.slices.cor,:));
2502 
+
2503 
+      if isfield(nii_view.handles,'coronal_bg') & ~isempty(nii_view.handles.coronal_bg)
2504 
+         set(nii_view.handles.coronal_bg,'CData',Scor');
2505 
+      else
2506 
+         axes(nii_view.handles.coronal_axes);
2507 
+
2508 
+         if useimagesc
2509 
+            nii_view.handles.coronal_bg = surface(zeros(size(Scor')),double(Scor'),'edgecolor','none','facecolor','interp');
2510 
+         else
2511 
+            nii_view.handles.coronal_bg = surface(zeros(size(Scor')),double(Scor'),'cdatamapping','direct','edgecolor','none','facecolor','interp');
2512 
+         end
2513 
+
2514 
+         order = get(gca,'child');
2515 
+         order(find(order == nii_view.handles.coronal_bg)) = [];
2516 
+         order = [order; nii_view.handles.coronal_bg];
2517 
+         set(gca, 'child', order);
2518 
+      end
2519 
+   end
2520 
+
2521 
+   if isfield(nii_view.handles,'coronal_image'),
2522 
+      if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
2523 
+         Scor = squeeze(nii_view.nii.img(:,nii_view.slices.cor,:,:,setscanid));
2524 
+         Scor = permute(Scor, [2 1 3]);
2525 
+      else
2526 
+         Scor = squeeze(nii_view.nii.img(:,nii_view.slices.cor,:,setscanid));
2527 
+         Scor = Scor';
2528 
+      end
2529 
+
2530 
+      set(nii_view.handles.coronal_image,'CData',Scor);
2531 
+   end
2532 
+
2533 
+   set(nii_view.handles.coronal_axes,'CLim',clim);
2534 
+
2535 
+   if ~isempty(nii_view.bgimg)
2536 
+      Ssag = squeeze(nii_view.bgimg(nii_view.slices.sag,:,:));
2537 
+
2538 
+      if isfield(nii_view.handles,'sagittal_bg') & ~isempty(nii_view.handles.sagittal_bg)
2539 
+         set(nii_view.handles.sagittal_bg,'CData',Ssag');
2540 
+      else
2541 
+         axes(nii_view.handles.sagittal_axes);
2542 
+
2543 
+         if useimagesc
2544 
+            nii_view.handles.sagittal_bg = surface(zeros(size(Ssag')),double(Ssag'),'edgecolor','none','facecolor','interp');
2545 
+         else
2546 
+            nii_view.handles.sagittal_bg = surface(zeros(size(Ssag')),double(Ssag'),'cdatamapping','direct','edgecolor','none','facecolor','interp');
2547 
+         end
2548 
+
2549 
+         order = get(gca,'child');
2550 
+         order(find(order == nii_view.handles.sagittal_bg)) = [];
2551 
+         order = [order; nii_view.handles.sagittal_bg];
2552 
+         set(gca, 'child', order);
2553 
+      end
2554 
+   end
2555 
+
2556 
+   if isfield(nii_view.handles,'sagittal_image'),
2557 
+      if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
2558 
+         Ssag = squeeze(nii_view.nii.img(nii_view.slices.sag,:,:,:,setscanid));
2559 
+         Ssag = permute(Ssag, [2 1 3]);
2560 
+      else
2561 
+         Ssag = squeeze(nii_view.nii.img(nii_view.slices.sag,:,:,setscanid));
2562 
+         Ssag = Ssag';
2563 
+      end
2564 
+
2565 
+      set(nii_view.handles.sagittal_image,'CData',Ssag);
2566 
+   end
2567 
+
2568 
+   set(nii_view.handles.sagittal_axes,'CLim',clim);
2569 
+
2570 
+   update_nii_view(nii_view);
2571 
+
2572 
+   if isfield(opt, 'setvalue')
2573 
+
2574 
+      if ~isfield(nii_view,'highcolor') | ~isequal(size(nii_view.highcolor),[56 3])
2575 
+
2576 
+         %  55 level for brain structure (paded 0 for highcolor level 1, i.e. normal level 201, to make 56 highcolor)
2577 
+         %
2578 
+         update_highcolor(fig, [zeros(1,3);gray(55)], []);
2579 
+
2580 
+      end
2581 
+
2582 
+      if nii_view.colorindex ~= 2
2583 
+         update_colorindex(fig, 2);
2584 
+      end
2585 
+
2586 
+      old_color = get(nii_view.handles.xhair_color,'user');
2587 
+
2588 
+      if isequal(old_color, [1 0 0])
2589 
+         update_crosshaircolor(fig, [1 1 0]);
2590 
+      end
2591 
+
2592 
+%      if change_interp
2593 
+ %        update_useinterp(fig, nii_view.useinterp);
2594 
+  %    end
2595 
+
2596 
+   end
2597 
+
2598 
+   if change_interp
2599 
+      update_useinterp(fig, nii_view.useinterp);
2600 
+   end
2601 
+
2602 
+   return;						% update_img
2603 
+
2604 
+
2605 
+%----------------------------------------------------------------
2606 
+function [top_pos, front_pos, side_pos] = ...
2607 
+			axes_pos(fig,area,vol_size,usestretch)
2608 
+
2609 
+   set(fig,'unit','pixel');
2610 
+
2611 
+   fig_pos = get(fig,'position');
2612 
+
2613 
+   gap_x = 15/fig_pos(3);		% width of vertical scrollbar
2614 
+   gap_y = 15/fig_pos(4);		% width of horizontal scrollbar
2615 
+
2616 
+   a = (area(3) - gap_x * 1.3) * fig_pos(3) / (vol_size(1) + vol_size(2));	% no crosshair lost in zoom
2617 
+   b = (area(4) - gap_y * 3) * fig_pos(4) / (vol_size(2) + vol_size(3));
2618 
+   c = min([a b]);			% make sure 'ax' is inside 'area'
2619 
+
2620 
+   top_w = vol_size(1) * c / fig_pos(3);
2621 
+   side_w = vol_size(2) * c / fig_pos(3);
2622 
+   top_h = vol_size(2) * c / fig_pos(4);
2623 
+   side_h = vol_size(3) * c / fig_pos(4);
2624 
+   side_x = area(1) + top_w + gap_x * 1.3;	% no crosshair lost in zoom
2625 
+   side_y = area(2) + top_h + gap_y * 3;
2626 
+
2627 
+   if usestretch
2628 
+      if a > b				% top touched ceiling, use b
2629 
+         d = (area(3) - gap_x * 1.3) / (top_w + side_w);	% no crosshair lost in zoom
2630 
+         top_w = top_w * d;
2631 
+         side_w = side_w * d;
2632 
+         side_x = area(1) + top_w + gap_x * 1.3;	% no crosshair lost in zoom
2633 
+      else
2634 
+         d = (area(4) - gap_y * 3) / (top_h + side_h);
2635 
+         top_h = top_h * d;
2636 
+         side_h = side_h * d;
2637 
+         side_y = area(2) + top_h + gap_y * 3;
2638 
+      end
2639 
+   end
2640 
+
2641 
+   top_pos = [area(1) area(2)+gap_y top_w top_h];
2642 
+   front_pos = [area(1) side_y top_w side_h];
2643 
+   side_pos = [side_x side_y side_w side_h];
2644 
+
2645 
+   set(fig,'unit','normal');
2646 
+
2647 
+   return;						% axes_pos
2648 
+
2649 
+
2650 
+%----------------------------------------------------------------
2651 
+function [top_ax, front_ax, side_ax] ...
2652 
+		= create_ax(fig, area, vol_size, usestretch)
2653 
+
2654 
+   cur_fig = gcf;			% save h_wait fig
2655 
+   figure(fig);
2656 
+
2657 
+   [top_pos, front_pos, side_pos] = ...
2658 
+			axes_pos(fig,area,vol_size,usestretch);
2659 
+
2660 
+   nii_view = getappdata(fig, 'nii_view');
2661 
+
2662 
+   if isempty(nii_view)
2663 
+      top_ax = axes('position', top_pos);
2664 
+      front_ax = axes('position', front_pos);
2665 
+      side_ax = axes('position', side_pos);
2666 
+   else
2667 
+      top_ax = nii_view.handles.axial_axes;
2668 
+      front_ax = nii_view.handles.coronal_axes;
2669 
+      side_ax = nii_view.handles.sagittal_axes;
2670 
+
2671 
+      set(top_ax, 'position', top_pos);
2672 
+      set(front_ax, 'position', front_pos);
2673 
+      set(side_ax, 'position', side_pos);
2674 
+   end
2675 
+
2676 
+   figure(cur_fig);
2677 
+
2678 
+   return;						% create_ax
2679 
+
2680 
+
2681 
+%----------------------------------------------------------------
2682 
+function [cbar_axes, cbarminmax_axes] = create_cbar_axes(fig, cbar_area, nii_view)
2683 
+
2684 
+   if isempty(cbar_area)		% without_cbar
2685 
+      cbar_axes = [];
2686 
+      cbarminmax_axes = [];
2687 
+      return;
2688 
+   end
2689 
+
2690 
+   cur_fig = gcf;			% save h_wait fig
2691 
+   figure(fig);
2692 
+
2693 
+   if ~exist('nii_view', 'var')
2694 
+      nii_view = getappdata(fig, 'nii_view');
2695 
+   end
2696 
+
2697 
+   if isempty(nii_view) | ~isfield(nii_view.handles,'cbar_axes') | isempty(nii_view.handles.cbar_axes)
2698 
+      cbarminmax_axes = axes('position', cbar_area);
2699 
+      cbar_axes = axes('position', cbar_area);
2700 
+   else
2701 
+      cbarminmax_axes = nii_view.handles.cbarminmax_axes;
2702 
+      cbar_axes = nii_view.handles.cbar_axes;
2703 
+      set(cbarminmax_axes, 'position', cbar_area);
2704 
+      set(cbar_axes, 'position', cbar_area);
2705 
+   end
2706 
+
2707 
+   figure(cur_fig);
2708 
+
2709 
+   return;					% create_cbar_axes
2710 
+
2711 
+
2712 
+%----------------------------------------------------------------
2713 
+function h1 = plot_view(fig, x, y, img_ax, img_slice, clim, ...
2714 
+	cbarminmax, handles, useimagesc, colorindex, color_map, ...
2715 
+	colorlevel, highcolor, useinterp, numscan)
2716 
+
2717 
+   h1 = [];
2718 
+
2719 
+   if x > 1 & y > 1,
2720 
+
2721 
+      axes(img_ax);
2722 
+
2723 
+      nii_view = getappdata(fig, 'nii_view');
2724 
+
2725 
+      if isempty(nii_view)
2726 
+
2727 
+         %  set colormap first
2728 
+         %
2729 
+         nii.handles = handles;
2730 
+         nii.handles.axial_axes = img_ax;
2731 
+         nii.colorindex = colorindex;
2732 
+         nii.color_map = color_map;
2733 
+         nii.colorlevel = colorlevel;
2734 
+         nii.highcolor = highcolor;
2735 
+         nii.numscan = numscan;
2736 
+
2737 
+         change_colormap(fig, nii, colorindex, cbarminmax);
2738 
+
2739 
+         if useinterp
2740 
+            if useimagesc
2741 
+               h1 = surface(zeros(size(img_slice)),double(img_slice),'edgecolor','none','facecolor','interp');
2742 
+            else
2743 
+               h1 = surface(zeros(size(img_slice)),double(img_slice),'cdatamapping','direct','edgecolor','none','facecolor','interp');
2744 
+            end
2745 
+
2746 
+            set(gca,'clim',clim);
2747 
+         else
2748 
+            if useimagesc
2749 
+               h1 = imagesc(img_slice,clim);
2750 
+            else
2751 
+               h1 = image(img_slice);
2752 
+            end
2753 
+
2754 
+            set(gca,'clim',clim);
2755 
+         end
2756 
+
2757 
+      else
2758 
+
2759 
+         h1 = nii_view.handles.axial_image;
2760 
+
2761 
+         if ~isequal(get(h1,'parent'), img_ax)
2762 
+            h1 = nii_view.handles.coronal_image;
2763 
+         end
2764 
+
2765 
+         if ~isequal(get(h1,'parent'), img_ax)
2766 
+            h1 = nii_view.handles.sagittal_image;
2767 
+         end
2768 
+
2769 
+         set(h1, 'cdata', img_slice);
2770 
+         set(h1, 'xdata', 1:size(img_slice,2));
2771 
+         set(h1, 'ydata', 1:size(img_slice,1));
2772 
+
2773 
+      end
2774 
+
2775 
+      set(img_ax,'YDir','normal','XLimMode','manual','YLimMode','manual',...
2776 
+         'ClimMode','manual','visible','off', ...
2777 
+         'xtick',[],'ytick',[], 'clim', clim);
2778 
+
2779 
+   end
2780 
+
2781 
+   return;						% plot_view
2782 
+
2783 
+
2784 
+%----------------------------------------------------------------
2785 
+function h1 = plot_cbar(fig, cbar_axes, cbarminmax_axes, cbarminmax, ...
2786 
+	level, handles, useimagesc, colorindex, color_map, ...
2787 
+	colorlevel, highcolor, niiclass, numscan, nii_view)
2788 
+
2789 
+   cbar_image = [1:level]';
2790 
+
2791 
+   %  In a uint8 or uint16 indexed image, 0 points to the first row
2792 
+   %  in the colormap
2793 
+   %
2794 
+   if 0 % strcmpi(niiclass,'uint8') | strcmpi(niiclass,'uint16')
2795 
+      % we use single for display anyway
2796 
+      ylim = [0, level-1];
2797 
+   else
2798 
+      ylim = [1, level];
2799 
+   end
2800 
+
2801 
+   axes(cbarminmax_axes);
2802 
+
2803 
+   plot([0 0], cbarminmax, 'w');
2804 
+   axis tight;
2805 
+
2806 
+   set(cbarminmax_axes,'YDir','normal', ...
2807 
+      'XLimMode','manual','YLimMode','manual','YColor',[0 0 0], ...
2808 
+      'XColor',[0 0 0],'xtick',[],'YAxisLocation','right');
2809 
+
2810 
+   ylimb = get(cbarminmax_axes,'ylim');
2811 
+   ytickb = get(cbarminmax_axes,'ytick');
2812 
+   ytick=(ylim(2)-ylim(1))*(ytickb-ylimb(1))/(ylimb(2)-ylimb(1))+ylim(1);
2813 
+
2814 
+   axes(cbar_axes);
2815 
+
2816 
+   if ~exist('nii_view', 'var')
2817 
+      nii_view = getappdata(fig, 'nii_view');
2818 
+   end
2819 
+
2820 
+   if isempty(nii_view) | ~isfield(nii_view.handles,'cbar_image') | isempty(nii_view.handles.cbar_image)
2821 
+
2822 
+      %  set colormap first
2823 
+      %
2824 
+      nii.handles = handles;
2825 
+      nii.colorindex = colorindex;
2826 
+      nii.color_map = color_map;
2827 
+      nii.colorlevel = colorlevel;
2828 
+      nii.highcolor = highcolor;
2829 
+      nii.numscan = numscan;
2830 
+
2831 
+      change_colormap(fig, nii, colorindex, cbarminmax);
2832 
+      h1 = image([0,1], [ylim(1),ylim(2)], cbar_image);
2833 
+
2834 
+   else
2835 
+      h1 = nii_view.handles.cbar_image;
2836 
+      set(h1, 'cdata', cbar_image);
2837 
+   end
2838 
+
2839 
+   set(cbar_axes,'YDir','normal','XLimMode','manual', ...
2840 
+	'YLimMode','manual','YColor',[0 0 0],'XColor',[0 0 0],'xtick',[], ...
2841 
+	'YAxisLocation','right','ylim',ylim,'ytick',ytick,'yticklabel','');
2842 
+
2843 
+   return;						% plot_cbar
2844 
+
2845 
+
2846 
+%----------------------------------------------------------------
2847 
+function set_coordinates(nii_view,useinterp)
2848 
+
2849 
+    imgPlim.vox = nii_view.dims;
2850 
+    imgNlim.vox = [1 1 1];
2851 
+
2852 
+    if useinterp
2853 
+       xdata_ax = [imgNlim.vox(1) imgPlim.vox(1)];
2854 
+       ydata_ax = [imgNlim.vox(2) imgPlim.vox(2)];
2855 
+       zdata_ax = [imgNlim.vox(3) imgPlim.vox(3)];
2856 
+    else
2857 
+       xdata_ax = [imgNlim.vox(1)-0.5 imgPlim.vox(1)+0.5];
2858 
+       ydata_ax = [imgNlim.vox(2)-0.5 imgPlim.vox(2)+0.5];
2859 
+       zdata_ax = [imgNlim.vox(3)-0.5 imgPlim.vox(3)+0.5];
2860 
+    end
2861 
+
2862 
+    if isfield(nii_view.handles,'axial_image') & ~isempty(nii_view.handles.axial_image)
2863 
+        set(nii_view.handles.axial_axes,'Xlim',xdata_ax);
2864 
+        set(nii_view.handles.axial_axes,'Ylim',ydata_ax);
2865 
+    end;
2866 
+    if isfield(nii_view.handles,'coronal_image') & ~isempty(nii_view.handles.coronal_image)
2867 
+        set(nii_view.handles.coronal_axes,'Xlim',xdata_ax);
2868 
+        set(nii_view.handles.coronal_axes,'Ylim',zdata_ax);
2869 
+    end;
2870 
+    if isfield(nii_view.handles,'sagittal_image') & ~isempty(nii_view.handles.sagittal_image)
2871 
+        set(nii_view.handles.sagittal_axes,'Xlim',ydata_ax);
2872 
+        set(nii_view.handles.sagittal_axes,'Ylim',zdata_ax);
2873 
+    end;
2874 
+
2875 
+    return						% set_coordinates
2876 
+
2877 
+
2878 
+%----------------------------------------------------------------
2879 
+function set_image_value(nii_view),
2880 
+
2881 
+    %  get coordinates of selected voxel and the image intensity there
2882 
+    %
2883 
+    sag = round(nii_view.slices.sag);
2884 
+    cor = round(nii_view.slices.cor);
2885 
+    axi = round(nii_view.slices.axi);
2886 
+
2887 
+    if 0 % isfield(nii_view, 'disp')
2888 
+       img = nii_view.disp;
2889 
+    else
2890 
+       img = nii_view.nii.img;
2891 
+    end
2892 
+
2893 
+    if nii_view.nii.hdr.dime.datatype == 128
2894 
+       imgvalue = [double(img(sag,cor,axi,1,nii_view.scanid)) double(img(sag,cor,axi,2,nii_view.scanid)) double(img(sag,cor,axi,3,nii_view.scanid))];
2895 
+       set(nii_view.handles.imval,'Value',imgvalue);
2896 
+       set(nii_view.handles.imval,'String',sprintf('%7.4g %7.4g %7.4g',imgvalue));
2897 
+    elseif nii_view.nii.hdr.dime.datatype == 511
2898 
+       R = double(img(sag,cor,axi,1,nii_view.scanid)) * (nii_view.nii.hdr.dime.glmax - ...
2899 
+		nii_view.nii.hdr.dime.glmin) + nii_view.nii.hdr.dime.glmin;
2900 
+       G = double(img(sag,cor,axi,2,nii_view.scanid)) * (nii_view.nii.hdr.dime.glmax - ...
2901 
+		nii_view.nii.hdr.dime.glmin) + nii_view.nii.hdr.dime.glmin;
2902 
+       B = double(img(sag,cor,axi,3,nii_view.scanid)) * (nii_view.nii.hdr.dime.glmax - ...
2903 
+		nii_view.nii.hdr.dime.glmin) + nii_view.nii.hdr.dime.glmin;
2904 
+       imgvalue = [double(img(sag,cor,axi,1,nii_view.scanid)) double(img(sag,cor,axi,2,nii_view.scanid)) double(img(sag,cor,axi,3,nii_view.scanid))];
2905 
+       set(nii_view.handles.imval,'Value',imgvalue);
2906 
+       imgvalue = [R G B];
2907 
+       set(nii_view.handles.imval,'String',sprintf('%7.4g %7.4g %7.4g',imgvalue));
2908 
+    else
2909 
+       imgvalue = double(img(sag,cor,axi,nii_view.scanid));
2910 
+       set(nii_view.handles.imval,'Value',imgvalue);
2911 
+
2912 
+       if isnan(imgvalue) | imgvalue > nii_view.cbarminmax(2)
2913 
+          imgvalue = 0;
2914 
+       end
2915 
+
2916 
+       set(nii_view.handles.imval,'String',sprintf('%.6g',imgvalue));
2917 
+    end
2918 
+
2919 
+    % Now update the coordinates of the selected voxel
2920 
+
2921 
+    nii_view = update_imgXYZ(nii_view);
2922 
+
2923 
+    if get(nii_view.handles.coord,'value') == 1,
2924 
+       sag = nii_view.imgXYZ.vox(1);
2925 
+       cor = nii_view.imgXYZ.vox(2);
2926 
+       axi = nii_view.imgXYZ.vox(3);
2927 
+       org = nii_view.origin;
2928 
+    elseif get(nii_view.handles.coord,'value') == 2,
2929 
+       sag = nii_view.imgXYZ.mm(1);
2930 
+       cor = nii_view.imgXYZ.mm(2);
2931 
+       axi = nii_view.imgXYZ.mm(3);
2932 
+       org = [0 0 0];
2933 
+    elseif get(nii_view.handles.coord,'value') == 3,
2934 
+       sag = nii_view.imgXYZ.tal(1);
2935 
+       cor = nii_view.imgXYZ.tal(2);
2936 
+       axi = nii_view.imgXYZ.tal(3);
2937 
+       org = [0 0 0];
2938 
+    end
2939 
+
2940 
+    set(nii_view.handles.impos,'Value',[sag,cor,axi]);
2941 
+
2942 
+    if get(nii_view.handles.coord,'value') == 1,
2943 
+        string = sprintf('%7.0f %7.0f %7.0f',sag,cor,axi);
2944 
+        org_str = sprintf('%7.0f %7.0f %7.0f', org(1), org(2), org(3));
2945 
+    else
2946 
+        string = sprintf('%7.1f %7.1f %7.1f',sag,cor,axi);
2947 
+        org_str = sprintf('%7.1f %7.1f %7.1f', org(1), org(2), org(3));
2948 
+    end;
2949 
+
2950 
+    set(nii_view.handles.impos,'String',string);
2951 
+    set(nii_view.handles.origin, 'string', org_str);
2952 
+
2953 
+    return						% set_image_value
2954 
+
2955 
+
2956 
+%----------------------------------------------------------------
2957 
+function nii_view = get_slice_position(nii_view,view),
2958 
+
2959 
+    %  obtain slices that is in correct unit, then update slices
2960 
+    %
2961 
+    slices = nii_view.slices;
2962 
+
2963 
+    switch view,
2964 
+    case 'sag',
2965 
+        currentpoint = get(nii_view.handles.sagittal_axes,'CurrentPoint');
2966 
+        slices.cor = currentpoint(1,1);
2967 
+        slices.axi = currentpoint(1,2);
2968 
+    case 'cor',
2969 
+        currentpoint = get(nii_view.handles.coronal_axes,'CurrentPoint');
2970 
+        slices.sag = currentpoint(1,1);
2971 
+        slices.axi = currentpoint(1,2);
2972 
+    case 'axi',
2973 
+        currentpoint = get(nii_view.handles.axial_axes,'CurrentPoint');
2974 
+        slices.sag = currentpoint(1,1);
2975 
+        slices.cor = currentpoint(1,2);
2976 
+    end
2977 
+
2978 
+    %  update nii_view.slices with the updated slices
2979 
+    %
2980 
+    nii_view.slices.axi = round(slices.axi);
2981 
+    nii_view.slices.cor = round(slices.cor);
2982 
+    nii_view.slices.sag = round(slices.sag);
2983 
+
2984 
+    return						% get_slice_position
2985 
+
2986 
+
2987 
+%----------------------------------------------------------------
2988 
+function nii_view = get_slider_position(nii_view),
2989 
+
2990 
+    [nii_view.slices.sag,nii_view.slices.cor,nii_view.slices.axi] = deal(0);
2991 
+
2992 
+    if isfield(nii_view.handles,'sagittal_slider'),
2993 
+        if ishandle(nii_view.handles.sagittal_slider),
2994 
+            nii_view.slices.sag = ...
2995 
+		round(get(nii_view.handles.sagittal_slider,'Value'));
2996 
+        end
2997 
+    end
2998 
+
2999 
+    if isfield(nii_view.handles,'coronal_slider'),
3000 
+        if ishandle(nii_view.handles.coronal_slider),
3001 
+            nii_view.slices.cor = ...
3002 
+		round(nii_view.dims(2) - ...
3003 
+		get(nii_view.handles.coronal_slider,'Value') + 1);
3004 
+        end
3005 
+    end
3006 
+
3007 
+    if isfield(nii_view.handles,'axial_slider'),
3008 
+        if ishandle(nii_view.handles.axial_slider),
3009 
+            nii_view.slices.axi = ...
3010 
+		round(get(nii_view.handles.axial_slider,'Value'));
3011 
+        end
3012 
+    end
3013 
+
3014 
+    nii_view = check_slices(nii_view);
3015 
+
3016 
+    return						% get_slider_position
3017 
+
3018 
+
3019 
+%----------------------------------------------------------------
3020 
+function nii_view = update_imgXYZ(nii_view),
3021 
+
3022 
+   nii_view.imgXYZ.vox = ...
3023 
+	[nii_view.slices.sag,nii_view.slices.cor,nii_view.slices.axi];
3024 
+   nii_view.imgXYZ.mm = ...
3025 
+	(nii_view.imgXYZ.vox - nii_view.origin) .* nii_view.voxel_size;
3026 
+%   nii_view.imgXYZ.tal = mni2tal(nii_view.imgXYZ.mni);
3027 
+
3028 
+   return						% update_imgXYZ
3029 
+
3030 
+
3031 
+%----------------------------------------------------------------
3032 
+function nii_view = convert2voxel(nii_view,slices),
3033 
+
3034 
+    if get(nii_view.handles.coord,'value') == 1,
3035 
+
3036 
+        %  [slices.axi, slices.cor, slices.sag] are in vox
3037 
+        %
3038 
+        nii_view.slices.axi = round(slices.axi);
3039 
+        nii_view.slices.cor = round(slices.cor);
3040 
+        nii_view.slices.sag = round(slices.sag);
3041 
+
3042 
+    elseif get(nii_view.handles.coord,'value') == 2,
3043 
+
3044 
+        %  [slices.axi, slices.cor, slices.sag] are in mm
3045 
+        %
3046 
+        xpix = nii_view.voxel_size(1);
3047 
+        ypix = nii_view.voxel_size(2);
3048 
+        zpix = nii_view.voxel_size(3);
3049 
+
3050 
+        nii_view.slices.axi = round(slices.axi / zpix + nii_view.origin(3));
3051 
+        nii_view.slices.cor = round(slices.cor / ypix + nii_view.origin(2));
3052 
+        nii_view.slices.sag = round(slices.sag / xpix + nii_view.origin(1));
3053 
+    elseif get(nii_view.handles.coord,'value') == 3,
3054 
+
3055 
+        %  [slices.axi, slices.cor, slices.sag] are in talairach
3056 
+        %
3057 
+        xpix = nii_view.voxel_size(1);
3058 
+        ypix = nii_view.voxel_size(2);
3059 
+        zpix = nii_view.voxel_size(3);
3060 
+
3061 
+        xyz_tal = [slices.sag, slices.cor, slices.axi];
3062 
+        xyz_mni = tal2mni(xyz_tal);
3063 
+
3064 
+        nii_view.slices.axi = round(xyz_mni(3) / zpix + nii_view.origin(3));
3065 
+        nii_view.slices.cor = round(xyz_mni(2) / ypix + nii_view.origin(2));
3066 
+        nii_view.slices.sag = round(xyz_mni(1) / xpix + nii_view.origin(1));
3067 
+
3068 
+    end
3069 
+
3070 
+    return						% convert2voxel
3071 
+
3072 
+
3073 
+%----------------------------------------------------------------
3074 
+function nii_view = check_slices(nii_view),
3075 
+
3076 
+    img = nii_view.nii.img;
3077 
+
3078 
+    [ SagSize, CorSize, AxiSize, TimeSize ] = size(img);
3079 
+    if nii_view.slices.sag > SagSize, nii_view.slices.sag = SagSize; end;
3080 
+    if nii_view.slices.sag < 1, nii_view.slices.sag = 1; end;
3081 
+    if nii_view.slices.cor > CorSize, nii_view.slices.cor = CorSize; end;
3082 
+    if nii_view.slices.cor < 1, nii_view.slices.cor = 1; end;
3083 
+    if nii_view.slices.axi > AxiSize, nii_view.slices.axi = AxiSize; end;
3084 
+    if nii_view.slices.axi < 1, nii_view.slices.axi = 1; end;
3085 
+    if nii_view.scanid > TimeSize, nii_view.scanid = TimeSize; end;
3086 
+    if nii_view.scanid < 1, nii_view.scanid = 1; end;
3087 
+
3088 
+    return						% check_slices
3089 
+
3090 
+
3091 
+%----------------------------------------------------------------
3092 
+%
3093 
+%  keep this function small, since it will be called for every click
3094 
+%
3095 
+function nii_view = update_nii_view(nii_view)
3096 
+
3097 
+   %  add imgXYZ into nii_view struct
3098 
+   %
3099 
+   nii_view = check_slices(nii_view);
3100 
+   nii_view = update_imgXYZ(nii_view);
3101 
+
3102 
+   %  update xhair
3103 
+   %
3104 
+   p_axi = nii_view.imgXYZ.vox([1 2]);
3105 
+   p_cor = nii_view.imgXYZ.vox([1 3]);
3106 
+   p_sag = nii_view.imgXYZ.vox([2 3]);
3107 
+
3108 
+   nii_view.axi_xhair = ...
3109 
+	rri_xhair(p_axi, nii_view.axi_xhair, nii_view.handles.axial_axes);
3110 
+
3111 
+   nii_view.cor_xhair = ...
3112 
+	rri_xhair(p_cor, nii_view.cor_xhair, nii_view.handles.coronal_axes);
3113 
+
3114 
+   nii_view.sag_xhair = ...
3115 
+	rri_xhair(p_sag, nii_view.sag_xhair, nii_view.handles.sagittal_axes);
3116 
+
3117 
+   setappdata(nii_view.fig, 'nii_view', nii_view);
3118 
+   set_image_value(nii_view);
3119 
+
3120 
+   return;						% update_nii_view
3121 
+
3122 
+
3123 
+%----------------------------------------------------------------
3124 
+function hist_plot(fig)
3125 
+
3126 
+   nii_view = getappdata(fig,'nii_view');
3127 
+
3128 
+   if isfield(nii_view, 'disp')
3129 
+      img = nii_view.disp;
3130 
+   else
3131 
+      img = nii_view.nii.img;
3132 
+   end
3133 
+
3134 
+   img = double(img(:));
3135 
+
3136 
+   if length(unique(round(img))) == length(unique(img))
3137 
+      is_integer = 1;
3138 
+      range = max(img) - min(img) + 1;
3139 
+      figure; hist(img, range);
3140 
+      set(gca, 'xlim', [-range/5, max(img)]);
3141 
+   else
3142 
+      is_integer = 0;
3143 
+      figure; hist(img);
3144 
+   end
3145 
+
3146 
+   xlabel('Voxel Intensity');
3147 
+   ylabel('Voxel Numbers for Each Intensity');
3148 
+   set(gcf, 'NumberTitle','off','Name','Histogram Plot');
3149 
+
3150 
+   return;						% hist_plot
3151 
+
3152 
+
3153 
+%----------------------------------------------------------------
3154 
+function hist_eq(fig)
3155 
+
3156 
+   nii_view = getappdata(fig,'nii_view');
3157 
+
3158 
+   old_pointer = get(fig,'Pointer');
3159 
+   set(fig,'Pointer','watch');
3160 
+
3161 
+   if get(nii_view.handles.hist_eq,'value')
3162 
+      max_img = double(max(nii_view.nii.img(:)));
3163 
+      tmp = double(nii_view.nii.img) / max_img;		% normalize for histeq
3164 
+      tmp = histeq(tmp(:));
3165 
+      nii_view.disp = reshape(tmp, size(nii_view.nii.img));
3166 
+      min_disp = min(nii_view.disp(:));
3167 
+      nii_view.disp = (nii_view.disp - min_disp);		% range having eq hist
3168 
+      nii_view.disp = nii_view.disp * max_img / max(nii_view.disp(:));
3169 
+      nii_view.disp = single(nii_view.disp);
3170 
+   else
3171 
+      if isfield(nii_view, 'disp')
3172 
+         nii_view.disp = nii_view.nii.img;
3173 
+      else
3174 
+         set(fig,'Pointer',old_pointer);
3175 
+         return;
3176 
+      end
3177 
+   end
3178 
+
3179 
+   %  update axial view
3180 
+   %
3181 
+   img_slice = squeeze(double(nii_view.disp(:,:,nii_view.slices.axi)));
3182 
+   h1 = nii_view.handles.axial_image;
3183 
+   set(h1, 'cdata', img_slice');
3184 
+
3185 
+   %  update coronal view
3186 
+   %
3187 
+   img_slice = squeeze(double(nii_view.disp(:,nii_view.slices.cor,:)));
3188 
+   h1 = nii_view.handles.coronal_image;
3189 
+   set(h1, 'cdata', img_slice');
3190 
+
3191 
+   %  update sagittal view
3192 
+   %
3193 
+   img_slice = squeeze(double(nii_view.disp(nii_view.slices.sag,:,:)));
3194 
+
3195 
+   h1 = nii_view.handles.sagittal_image;
3196 
+   set(h1, 'cdata', img_slice');
3197 
+
3198 
+   %  remove disp field if un-check 'histeq' button
3199 
+   %
3200 
+   if ~get(nii_view.handles.hist_eq,'value') & isfield(nii_view, 'disp')
3201 
+      nii_view = rmfield(nii_view, 'disp');
3202 
+   end
3203 
+
3204 
+   update_nii_view(nii_view);
3205 
+
3206 
+   set(fig,'Pointer',old_pointer);
3207 
+
3208 
+   return;						% hist_eq
3209 
+
3210 
+
3211 
+%----------------------------------------------------------------
3212 
+function [top1_label, top2_label, side1_label, side2_label] = ...
3213 
+		dir_label(fig, top_ax, front_ax, side_ax)
3214 
+
3215 
+   nii_view = getappdata(fig,'nii_view');
3216 
+
3217 
+   top_pos = get(top_ax,'position');
3218 
+   front_pos = get(front_ax,'position');
3219 
+   side_pos = get(side_ax,'position');
3220 
+
3221 
+   top_gap_x = (side_pos(1)-top_pos(1)-top_pos(3)) / (2*top_pos(3));
3222 
+   top_gap_y = (front_pos(2)-top_pos(2)-top_pos(4)) / (2*top_pos(4));
3223 
+   side_gap_x = (side_pos(1)-top_pos(1)-top_pos(3)) / (2*side_pos(3));
3224 
+   side_gap_y = (front_pos(2)-top_pos(2)-top_pos(4)) / (2*side_pos(4));
3225 
+
3226 
+   top1_label_pos = [0, 1];			% rot0
3227 
+   top2_label_pos = [1, 0];			% rot90
3228 
+   side1_label_pos = [1, - side_gap_y];		% rot0
3229 
+   side2_label_pos = [0, 0];			% rot90
3230 
+
3231 
+   if isempty(nii_view)
3232 
+      axes(top_ax);
3233 
+      top1_label = text(top1_label_pos(1),top1_label_pos(2), ...
3234 
+	'== X =>', ...
3235 
+	'vertical', 'bottom', ...
3236 
+	'unit', 'normal', 'fontsize', 8);
3237 
+
3238 
+      axes(top_ax);
3239 
+      top2_label = text(top2_label_pos(1),top2_label_pos(2), ...
3240 
+	'== Y =>', ...
3241 
+	'rotation', 90, 'vertical', 'top', ...
3242 
+	'unit', 'normal', 'fontsize', 8);
3243 
+
3244 
+      axes(side_ax);
3245 
+      side1_label = text(side1_label_pos(1),side1_label_pos(2), ...
3246 
+	'<= Y ==', ...
3247 
+	'horizontal', 'right', 'vertical', 'top', ...
3248 
+	'unit', 'normal', 'fontsize', 8);
3249 
+
3250 
+      axes(side_ax);
3251 
+      side2_label = text(side2_label_pos(1),side2_label_pos(2), ...
3252 
+	'== Z =>', ...
3253 
+	'rotation', 90, 'vertical', 'bottom', ...
3254 
+	'unit', 'normal', 'fontsize', 8);
3255 
+   else
3256 
+      top1_label = nii_view.handles.top1_label;
3257 
+      top2_label = nii_view.handles.top2_label;
3258 
+      side1_label = nii_view.handles.side1_label;
3259 
+      side2_label = nii_view.handles.side2_label;
3260 
+
3261 
+      set(top1_label, 'position', [top1_label_pos 0]);
3262 
+      set(top2_label, 'position', [top2_label_pos 0]);
3263 
+      set(side1_label, 'position', [side1_label_pos 0]);
3264 
+      set(side2_label, 'position', [side2_label_pos 0]);
3265 
+   end
3266 
+
3267 
+   return;						% dir_label
3268 
+
3269 
+
3270 
+%----------------------------------------------------------------
3271 
+function update_enable(h, opt);
3272 
+
3273 
+   nii_view = getappdata(h,'nii_view');
3274 
+   handles = nii_view.handles;
3275 
+
3276 
+   if isfield(opt,'enablecursormove')
3277 
+      if opt.enablecursormove
3278 
+         v = 'on';
3279 
+      else
3280 
+         v = 'off';
3281 
+      end
3282 
+
3283 
+      set(handles.Timposcur, 'visible', v);
3284 
+      set(handles.imposcur, 'visible', v);
3285 
+      set(handles.Timvalcur, 'visible', v);
3286 
+      set(handles.imvalcur, 'visible', v);
3287 
+   end
3288 
+
3289 
+   if isfield(opt,'enableviewpoint')
3290 
+      if opt.enableviewpoint
3291 
+         v = 'on';
3292 
+      else
3293 
+         v = 'off';
3294 
+      end
3295 
+
3296 
+      set(handles.Timpos, 'visible', v);
3297 
+      set(handles.impos, 'visible', v);
3298 
+      set(handles.Timval, 'visible', v);
3299 
+      set(handles.imval, 'visible', v);
3300 
+   end
3301 
+
3302 
+   if isfield(opt,'enableorigin')
3303 
+      if opt.enableorigin
3304 
+         v = 'on';
3305 
+      else
3306 
+         v = 'off';
3307 
+      end
3308 
+
3309 
+      set(handles.Torigin, 'visible', v);
3310 
+      set(handles.origin, 'visible', v);
3311 
+   end
3312 
+
3313 
+   if isfield(opt,'enableunit')
3314 
+      if opt.enableunit
3315 
+         v = 'on';
3316 
+      else
3317 
+         v = 'off';
3318 
+      end
3319 
+
3320 
+      set(handles.Tcoord, 'visible', v);
3321 
+      set(handles.coord_frame, 'visible', v);
3322 
+      set(handles.coord, 'visible', v);
3323 
+   end
3324 
+
3325 
+   if isfield(opt,'enablecrosshair')
3326 
+      if opt.enablecrosshair
3327 
+         v = 'on';
3328 
+      else
3329 
+         v = 'off';
3330 
+      end
3331 
+
3332 
+      set(handles.Txhair, 'visible', v);
3333 
+      set(handles.xhair_color, 'visible', v);
3334 
+      set(handles.xhair, 'visible', v);
3335 
+   end
3336 
+
3337 
+   if isfield(opt,'enablehistogram')
3338 
+      if opt.enablehistogram
3339 
+         v = 'on';
3340 
+         vv = 'off';
3341 
+      else
3342 
+         v = 'off';
3343 
+         vv = 'on';
3344 
+      end
3345 
+
3346 
+      set(handles.Tcoord, 'visible', vv);
3347 
+      set(handles.coord_frame, 'visible', vv);
3348 
+      set(handles.coord, 'visible', vv);
3349 
+
3350 
+      set(handles.Thist, 'visible', v);
3351 
+      set(handles.hist_frame, 'visible', v);
3352 
+      set(handles.hist_eq, 'visible', v);
3353 
+      set(handles.hist_plot, 'visible', v);
3354 
+   end
3355 
+
3356 
+   if isfield(opt,'enablecolormap')
3357 
+      if opt.enablecolormap
3358 
+         v = 'on';
3359 
+      else
3360 
+         v = 'off';
3361 
+      end
3362 
+
3363 
+      set(handles.Tcolor, 'visible', v);
3364 
+      set(handles.color_frame, 'visible', v);
3365 
+      set(handles.neg_color, 'visible', v);
3366 
+      set(handles.colorindex, 'visible', v);
3367 
+   end
3368 
+
3369 
+   if isfield(opt,'enablecontrast')
3370 
+      if opt.enablecontrast
3371 
+         v = 'on';
3372 
+      else
3373 
+         v = 'off';
3374 
+      end
3375 
+
3376 
+      set(handles.Tcontrast, 'visible', v);
3377 
+      set(handles.contrast_frame, 'visible', v);
3378 
+      set(handles.contrast_def, 'visible', v);
3379 
+      set(handles.contrast, 'visible', v);
3380 
+   end
3381 
+
3382 
+   if isfield(opt,'enablebrightness')
3383 
+      if opt.enablebrightness
3384 
+         v = 'on';
3385 
+      else
3386 
+         v = 'off';
3387 
+      end
3388 
+
3389 
+      set(handles.Tbrightness, 'visible', v);
3390 
+      set(handles.brightness_frame, 'visible', v);
3391 
+      set(handles.brightness_def, 'visible', v);
3392 
+      set(handles.brightness, 'visible', v);
3393 
+   end
3394 
+
3395 
+   if isfield(opt,'enabledirlabel')
3396 
+      if opt.enabledirlabel
3397 
+         v = 'on';
3398 
+      else
3399 
+         v = 'off';
3400 
+      end
3401 
+
3402 
+      set(handles.top1_label, 'visible', v);
3403 
+      set(handles.top2_label, 'visible', v);
3404 
+      set(handles.side1_label, 'visible', v);
3405 
+      set(handles.side2_label, 'visible', v);
3406 
+   end
3407 
+
3408 
+   if isfield(opt,'enableslider')
3409 
+      if opt.enableslider
3410 
+         v = 'on';
3411 
+      else
3412 
+         v = 'off';
3413 
+      end
3414 
+
3415 
+      if isfield(handles,'sagittal_slider') & ishandle(handles.sagittal_slider)
3416 
+         set(handles.sagittal_slider, 'visible', v);
3417 
+      end
3418 
+
3419 
+      if isfield(handles,'coronal_slider') & ishandle(handles.coronal_slider)
3420 
+         set(handles.coronal_slider, 'visible', v);
3421 
+      end
3422 
+
3423 
+      if isfield(handles,'axial_slider') & ishandle(handles.axial_slider)
3424 
+         set(handles.axial_slider, 'visible', v);
3425 
+      end
3426 
+   end
3427 
+
3428 
+   return;					% update_enable
3429 
+
3430 
+
3431 
+%----------------------------------------------------------------
3432 
+function update_usepanel(fig, usepanel)
3433 
+
3434 
+   if isempty(usepanel)
3435 
+      return;
3436 
+   end
3437 
+
3438 
+   if usepanel
3439 
+      opt.enablecursormove = 1;
3440 
+      opt.enableviewpoint = 1;
3441 
+      opt.enableorigin = 1;
3442 
+      opt.enableunit = 1;
3443 
+      opt.enablecrosshair = 1;
3444 
+%      opt.enablehistogram = 1;
3445 
+      opt.enablecolormap = 1;
3446 
+      opt.enablecontrast = 1;
3447 
+      opt.enablebrightness = 1;
3448 
+   else
3449 
+      opt.enablecursormove = 0;
3450 
+      opt.enableviewpoint = 0;
3451 
+      opt.enableorigin = 0;
3452 
+      opt.enableunit = 0;
3453 
+      opt.enablecrosshair = 0;
3454 
+%      opt.enablehistogram = 0;
3455 
+      opt.enablecolormap = 0;
3456 
+      opt.enablecontrast = 0;
3457 
+      opt.enablebrightness = 0;
3458 
+   end
3459 
+
3460 
+   update_enable(fig, opt);
3461 
+
3462 
+   nii_view = getappdata(fig,'nii_view');
3463 
+   nii_view.usepanel = usepanel;
3464 
+   setappdata(fig,'nii_view',nii_view);
3465 
+
3466 
+   return;					% update_usepanel
3467 
+
3468 
+
3469 
+%----------------------------------------------------------------
3470 
+function update_usecrosshair(fig, usecrosshair)
3471 
+
3472 
+   if isempty(usecrosshair)
3473 
+      return;
3474 
+   end
3475 
+
3476 
+   if usecrosshair
3477 
+      v=1;
3478 
+   else
3479 
+      v=2;
3480 
+   end
3481 
+
3482 
+   nii_view = getappdata(fig,'nii_view');
3483 
+   set(nii_view.handles.xhair,'value',v);
3484 
+
3485 
+   opt.command = 'crosshair';
3486 
+   view_nii(fig, opt);
3487 
+
3488 
+   return;					% update_usecrosshair
3489 
+
3490 
+
3491 
+%----------------------------------------------------------------
3492 
+function update_usestretch(fig, usestretch)
3493 
+
3494 
+   nii_view = getappdata(fig,'nii_view');
3495 
+
3496 
+   handles = nii_view.handles;
3497 
+   fig = nii_view.fig;
3498 
+   area = nii_view.area;
3499 
+   vol_size = nii_view.voxel_size .* nii_view.dims;
3500 
+
3501 
+   %  Three Axes & label
3502 
+   %
3503 
+   [top_ax, front_ax, side_ax] = ...
3504 
+	create_ax(fig, area, vol_size, usestretch);
3505 
+
3506 
+   dir_label(fig, top_ax, front_ax, side_ax);
3507 
+
3508 
+   top_pos = get(top_ax,'position');
3509 
+   front_pos = get(front_ax,'position');
3510 
+   side_pos = get(side_ax,'position');
3511 
+
3512 
+   %  Sagittal Slider
3513 
+   %
3514 
+   x = side_pos(1);
3515 
+   y = top_pos(2) + top_pos(4);
3516 
+   w = side_pos(3);
3517 
+   h = (front_pos(2) - y) / 2;
3518 
+   y = y + h;
3519 
+   pos = [x y w h];
3520 
+
3521 
+   if isfield(handles,'sagittal_slider') & ishandle(handles.sagittal_slider)
3522 
+      set(handles.sagittal_slider,'position',pos);
3523 
+   end
3524 
+
3525 
+   %  Coronal Slider
3526 
+   %
3527 
+   x = top_pos(1);
3528 
+   y = top_pos(2) + top_pos(4);
3529 
+   w = top_pos(3);
3530 
+   h = (front_pos(2) - y) / 2;
3531 
+   y = y + h;
3532 
+   pos = [x y w h];
3533 
+
3534 
+   if isfield(handles,'coronal_slider') & ishandle(handles.coronal_slider)
3535 
+      set(handles.coronal_slider,'position',pos);
3536 
+   end
3537 
+
3538 
+   %  Axial Slider
3539 
+   %
3540 
+   x = top_pos(1);
3541 
+   y = area(2);
3542 
+   w = top_pos(3);
3543 
+   h = top_pos(2) - y;
3544 
+   pos = [x y w h];
3545 
+
3546 
+   if isfield(handles,'axial_slider') & ishandle(handles.axial_slider)
3547 
+      set(handles.axial_slider,'position',pos);
3548 
+   end
3549 
+
3550 
+   %  plot info view
3551 
+   %
3552 
+%   info_pos = [side_pos([1,3]); top_pos([2,4])];
3553 
+%   info_pos = info_pos(:);
3554 
+   gap = side_pos(1)-(top_pos(1)+top_pos(3));
3555 
+   info_pos(1) = side_pos(1) + gap;
3556 
+   info_pos(2) = area(2);
3557 
+   info_pos(3) = side_pos(3) - gap;
3558 
+   info_pos(4) = top_pos(2) + top_pos(4) - area(2) - gap;
3559 
+
3560 
+   num_inputline = 10;
3561 
+   inputline_space =info_pos(4) / num_inputline;
3562 
+
3563 
+
3564 
+   %  Image Intensity Value at Cursor
3565 
+   %
3566 
+   x = info_pos(1);
3567 
+   y = info_pos(2);
3568 
+   w = info_pos(3)*0.5;
3569 
+   h = inputline_space*0.6;
3570 
+
3571 
+   pos = [x y w h];
3572 
+   set(handles.Timvalcur,'position',pos);
3573 
+
3574 
+   x = x + w;
3575 
+   w = info_pos(3)*0.5;
3576 
+
3577 
+   pos = [x y w h];
3578 
+   set(handles.imvalcur,'position',pos);
3579 
+
3580 
+   %  Position at Cursor
3581 
+   %
3582 
+   x = info_pos(1);
3583 
+   y = y + inputline_space;
3584 
+   w = info_pos(3)*0.5;
3585 
+
3586 
+   pos = [x y w h];
3587 
+   set(handles.Timposcur,'position',pos);
3588 
+
3589 
+   x = x + w;
3590 
+   w = info_pos(3)*0.5;
3591 
+
3592 
+   pos = [x y w h];
3593 
+   set(handles.imposcur,'position',pos);
3594 
+
3595 
+   %  Image Intensity Value at Mouse Click
3596 
+   %
3597 
+   x = info_pos(1);
3598 
+   y = y + inputline_space;
3599 
+   w = info_pos(3)*0.5;
3600 
+
3601 
+   pos = [x y w h];
3602 
+   set(handles.Timval,'position',pos);
3603 
+
3604 
+   x = x + w;
3605 
+   w = info_pos(3)*0.5;
3606 
+
3607 
+   pos = [x y w h];
3608 
+   set(handles.imval,'position',pos);
3609 
+
3610 
+   %  Viewpoint Position at Mouse Click
3611 
+   %
3612 
+   x = info_pos(1);
3613 
+   y = y + inputline_space;
3614 
+   w = info_pos(3)*0.5;
3615 
+
3616 
+   pos = [x y w h];
3617 
+   set(handles.Timpos,'position',pos);
3618 
+
3619 
+   x = x + w + 0.005;
3620 
+   y = y - 0.008;
3621 
+   w = info_pos(3)*0.5;
3622 
+   h = inputline_space*0.9;
3623 
+
3624 
+   pos = [x y w h];
3625 
+   set(handles.impos,'position',pos);
3626 
+
3627 
+   %  Origin Position
3628 
+   %
3629 
+   x = info_pos(1);
3630 
+   y = y + inputline_space*1.2;
3631 
+   w = info_pos(3)*0.5;
3632 
+   h = inputline_space*0.6;
3633 
+
3634 
+   pos = [x y w h];
3635 
+   set(handles.Torigin,'position',pos);
3636 
+
3637 
+   x = x + w;
3638 
+   w = info_pos(3)*0.5;
3639 
+
3640 
+   pos = [x y w h];
3641 
+   set(handles.origin,'position',pos);
3642 
+
3643 
+if 0
3644 
+   %  Axes Unit
3645 
+   %
3646 
+   x = info_pos(1);
3647 
+   y = y + inputline_space;
3648 
+   w = info_pos(3)*0.5;
3649 
+
3650 
+   pos = [x y w h];
3651 
+   set(handles.Tcoord,'position',pos);
3652 
+
3653 
+   x = x + w + 0.005;
3654 
+   w = info_pos(3)*0.5 - 0.005;
3655 
+
3656 
+   pos = [x y w h];
3657 
+   set(handles.coord,'position',pos);
3658 
+end
3659 
+
3660 
+   %  Crosshair
3661 
+   %
3662 
+   x = info_pos(1);
3663 
+   y = y + inputline_space;
3664 
+   w = info_pos(3)*0.4;
3665 
+
3666 
+   pos = [x y w h];
3667 
+   set(handles.Txhair,'position',pos);
3668 
+
3669 
+   x = info_pos(1) + info_pos(3)*0.5;
3670 
+   w = info_pos(3)*0.2;
3671 
+   h = inputline_space*0.7;
3672 
+
3673 
+   pos = [x y w h];
3674 
+   set(handles.xhair_color,'position',pos);
3675 
+
3676 
+   x = info_pos(1) + info_pos(3)*0.7;
3677 
+   w = info_pos(3)*0.3;
3678 
+
3679 
+   pos = [x y w h];
3680 
+   set(handles.xhair,'position',pos);
3681 
+
3682 
+   %  Histogram & Color
3683 
+   %
3684 
+   x = info_pos(1);
3685 
+   w = info_pos(3)*0.45;
3686 
+   h = inputline_space * 1.5;
3687 
+   pos = [x,  y+inputline_space*0.9,  w,  h];
3688 
+   set(handles.hist_frame,'position',pos);
3689 
+   set(handles.coord_frame,'position',pos);
3690 
+
3691 
+   x = info_pos(1) + info_pos(3)*0.475;
3692 
+   w = info_pos(3)*0.525;
3693 
+   h = inputline_space * 1.5;
3694 
+
3695 
+   pos = [x,  y+inputline_space*0.9,  w,  h];
3696 
+   set(handles.color_frame,'position',pos);
3697 
+
3698 
+   x = info_pos(1) + info_pos(3)*0.025;
3699 
+   y = y + inputline_space*1.2;
3700 
+   w = info_pos(3)*0.2;
3701 
+   h = inputline_space*0.7;
3702 
+
3703 
+   pos = [x y w h];
3704 
+   set(handles.hist_eq,'position',pos);
3705 
+
3706 
+   x = x + w;
3707 
+   w = info_pos(3)*0.2;
3708 
+
3709 
+   pos = [x y w h];
3710 
+   set(handles.hist_plot,'position',pos);
3711 
+
3712 
+   x = info_pos(1) + info_pos(3)*0.025;
3713 
+   w = info_pos(3)*0.4;
3714 
+
3715 
+   pos = [x y w h];
3716 
+   set(handles.coord,'position',pos);
3717 
+
3718 
+   x = info_pos(1) + info_pos(3)*0.5;
3719 
+   w = info_pos(3)*0.2;
3720 
+   pos = [x y w h];
3721 
+   set(handles.neg_color,'position',pos);
3722 
+
3723 
+   x = info_pos(1) + info_pos(3)*0.7;
3724 
+   w = info_pos(3)*0.275;
3725 
+
3726 
+   pos = [x y w h];
3727 
+   set(handles.colorindex,'position',pos);
3728 
+
3729 
+   x = info_pos(1) + info_pos(3)*0.1;
3730 
+   y = y + inputline_space;
3731 
+   w = info_pos(3)*0.28;
3732 
+   h = inputline_space*0.6;
3733 
+
3734 
+   pos = [x y w h];
3735 
+   set(handles.Thist,'position',pos);
3736 
+   set(handles.Tcoord,'position',pos);
3737 
+
3738 
+   x = info_pos(1) + info_pos(3)*0.60;
3739 
+   w = info_pos(3)*0.28;
3740 
+
3741 
+   pos = [x y w h];
3742 
+   set(handles.Tcolor,'position',pos);
3743 
+
3744 
+   %  Contrast Frame
3745 
+   %
3746 
+   x = info_pos(1);
3747 
+   w = info_pos(3)*0.45;
3748 
+   h = inputline_space * 2;
3749 
+
3750 
+   pos = [x,  y+inputline_space*0.8,  w,  h];
3751 
+   set(handles.contrast_frame,'position',pos);
3752 
+
3753 
+   %  Brightness Frame
3754 
+   %
3755 
+   x = info_pos(1) + info_pos(3)*0.475;
3756 
+   w = info_pos(3)*0.525;
3757 
+
3758 
+   pos = [x,  y+inputline_space*0.8,  w,  h];
3759 
+   set(handles.brightness_frame,'position',pos);
3760 
+
3761 
+   %  Contrast
3762 
+   %
3763 
+   x = info_pos(1) + info_pos(3)*0.025;
3764 
+   y = y + inputline_space;
3765 
+   w = info_pos(3)*0.4;
3766 
+   h = inputline_space*0.6;
3767 
+
3768 
+   pos = [x y w h];
3769 
+   set(handles.contrast,'position',pos);
3770 
+
3771 
+   %  Brightness
3772 
+   %
3773 
+   x = info_pos(1) + info_pos(3)*0.5;
3774 
+   w = info_pos(3)*0.475;
3775 
+
3776 
+   pos = [x y w h];
3777 
+   set(handles.brightness,'position',pos);
3778 
+
3779 
+   %  Contrast text/def
3780 
+   %
3781 
+   x = info_pos(1) + info_pos(3)*0.025;
3782 
+   y = y + inputline_space;
3783 
+   w = info_pos(3)*0.22;
3784 
+
3785 
+   pos = [x y w h];
3786 
+   set(handles.Tcontrast,'position',pos);
3787 
+
3788 
+   x = x + w;
3789 
+   w = info_pos(3)*0.18;
3790 
+
3791 
+   pos = [x y w h];
3792 
+   set(handles.contrast_def,'position',pos);
3793 
+
3794 
+   %  Brightness text/def
3795 
+   %
3796 
+   x = info_pos(1) + info_pos(3)*0.5;
3797 
+   w = info_pos(3)*0.295;
3798 
+
3799 
+   pos = [x y w h];
3800 
+   set(handles.Tbrightness,'position',pos);
3801 
+
3802 
+   x = x + w;
3803 
+   w = info_pos(3)*0.18;
3804 
+
3805 
+   pos = [x y w h];
3806 
+   set(handles.brightness_def,'position',pos);
3807 
+
3808 
+   return;					% update_usestretch
3809 
+
3810 
+
3811 
+%----------------------------------------------------------------
3812 
+function update_useinterp(fig, useinterp)
3813 
+
3814 
+   if isempty(useinterp)
3815 
+      return;
3816 
+   end
3817 
+
3818 
+   nii_menu = getappdata(fig, 'nii_menu');
3819 
+
3820 
+   if ~isempty(nii_menu)
3821 
+      if get(nii_menu.Minterp,'user')
3822 
+         set(nii_menu.Minterp,'Userdata',0,'Label','Interp off');
3823 
+      else
3824 
+         set(nii_menu.Minterp,'Userdata',1,'Label','Interp on');
3825 
+      end
3826 
+   end
3827 
+
3828 
+   nii_view = getappdata(fig, 'nii_view');
3829 
+   nii_view.useinterp = useinterp;
3830 
+
3831 
+   if ~isempty(nii_view.handles.axial_image)
3832 
+      if strcmpi(get(nii_view.handles.axial_image,'cdatamapping'), 'direct')
3833 
+         useimagesc = 0;
3834 
+      else
3835 
+         useimagesc = 1;
3836 
+      end
3837 
+   elseif ~isempty(nii_view.handles.coronal_image)
3838 
+      if strcmpi(get(nii_view.handles.coronal_image,'cdatamapping'), 'direct')
3839 
+         useimagesc = 0;
3840 
+      else
3841 
+         useimagesc = 1;
3842 
+      end
3843 
+   else
3844 
+      if strcmpi(get(nii_view.handles.sagittal_image,'cdatamapping'), 'direct')
3845 
+         useimagesc = 0;
3846 
+      else
3847 
+         useimagesc = 1;
3848 
+      end
3849 
+   end
3850 
+
3851 
+   if ~isempty(nii_view.handles.axial_image)
3852 
+      img_slice = get(nii_view.handles.axial_image, 'cdata');
3853 
+      delete(nii_view.handles.axial_image);
3854 
+      axes(nii_view.handles.axial_axes);
3855 
+      clim = get(gca,'clim');
3856 
+
3857 
+      if useinterp
3858 
+         if useimagesc
3859 
+            nii_view.handles.axial_image = surface(zeros(size(img_slice)),double(img_slice),'edgecolor','none','facecolor','interp');
3860 
+         else
3861 
+            nii_view.handles.axial_image = surface(zeros(size(img_slice)),double(img_slice),'cdatamapping','direct','edgecolor','none','facecolor','interp');
3862 
+         end
3863 
+      else
3864 
+         if useimagesc
3865 
+            nii_view.handles.axial_image = imagesc('cdata',img_slice);
3866 
+         else
3867 
+            nii_view.handles.axial_image = image('cdata',img_slice);
3868 
+         end
3869 
+      end
3870 
+
3871 
+      set(gca,'clim',clim);
3872 
+
3873 
+      order = get(gca,'child');
3874 
+      order(find(order == nii_view.handles.axial_image)) = [];
3875 
+      order = [order; nii_view.handles.axial_image];
3876 
+
3877 
+      if isfield(nii_view.handles,'axial_bg') & ~isempty(nii_view.handles.axial_bg)
3878 
+         order(find(order == nii_view.handles.axial_bg)) = [];
3879 
+         order = [order; nii_view.handles.axial_bg];
3880 
+      end
3881 
+
3882 
+      set(gca, 'child', order);
3883 
+
3884 
+      if ~useinterp
3885 
+         if isfield(nii_view.handles,'axial_bg') & ~isempty(nii_view.handles.axial_bg)
3886 
+            delete(nii_view.handles.axial_bg);
3887 
+            nii_view.handles.axial_bg = [];
3888 
+         end
3889 
+      end
3890 
+
3891 
+      set(nii_view.handles.axial_image,'buttondown','view_nii(''axial_image'');');
3892 
+   end
3893 
+
3894 
+   if ~isempty(nii_view.handles.coronal_image)
3895 
+      img_slice = get(nii_view.handles.coronal_image, 'cdata');
3896 
+      delete(nii_view.handles.coronal_image);
3897 
+      axes(nii_view.handles.coronal_axes);
3898 
+      clim = get(gca,'clim');
3899 
+
3900 
+      if useinterp
3901 
+         if useimagesc
3902 
+            nii_view.handles.coronal_image = surface(zeros(size(img_slice)),double(img_slice),'edgecolor','none','facecolor','interp');
3903 
+         else
3904 
+            nii_view.handles.coronal_image = surface(zeros(size(img_slice)),double(img_slice),'cdatamapping','direct','edgecolor','none','facecolor','interp');
3905 
+         end
3906 
+      else
3907 
+         if useimagesc
3908 
+            nii_view.handles.coronal_image = imagesc('cdata',img_slice);
3909 
+         else
3910 
+            nii_view.handles.coronal_image = image('cdata',img_slice);
3911 
+         end
3912 
+      end
3913 
+
3914 
+      set(gca,'clim',clim);
3915 
+
3916 
+      order = get(gca,'child');
3917 
+      order(find(order == nii_view.handles.coronal_image)) = [];
3918 
+      order = [order; nii_view.handles.coronal_image];
3919 
+
3920 
+      if isfield(nii_view.handles,'coronal_bg') & ~isempty(nii_view.handles.coronal_bg)
3921 
+         order(find(order == nii_view.handles.coronal_bg)) = [];
3922 
+         order = [order; nii_view.handles.coronal_bg];
3923 
+      end
3924 
+
3925 
+      set(gca, 'child', order);
3926 
+
3927 
+      if ~useinterp
3928 
+         if isfield(nii_view.handles,'coronal_bg') & ~isempty(nii_view.handles.coronal_bg)
3929 
+            delete(nii_view.handles.coronal_bg);
3930 
+            nii_view.handles.coronal_bg = [];
3931 
+         end
3932 
+      end
3933 
+
3934 
+      set(nii_view.handles.coronal_image,'buttondown','view_nii(''coronal_image'');');
3935 
+   end
3936 
+
3937 
+   if ~isempty(nii_view.handles.sagittal_image)
3938 
+      img_slice = get(nii_view.handles.sagittal_image, 'cdata');
3939 
+      delete(nii_view.handles.sagittal_image);
3940 
+      axes(nii_view.handles.sagittal_axes);
3941 
+      clim = get(gca,'clim');
3942 
+
3943 
+      if useinterp
3944 
+         if useimagesc
3945 
+            nii_view.handles.sagittal_image = surface(zeros(size(img_slice)),double(img_slice),'edgecolor','none','facecolor','interp');
3946 
+         else
3947 
+            nii_view.handles.sagittal_image = surface(zeros(size(img_slice)),double(img_slice),'cdatamapping','direct','edgecolor','none','facecolor','interp');
3948 
+         end
3949 
+      else
3950 
+         if useimagesc
3951 
+            nii_view.handles.sagittal_image = imagesc('cdata',img_slice);
3952 
+         else
3953 
+            nii_view.handles.sagittal_image = image('cdata',img_slice);
3954 
+         end
3955 
+      end
3956 
+
3957 
+      set(gca,'clim',clim);
3958 
+
3959 
+      order = get(gca,'child');
3960 
+      order(find(order == nii_view.handles.sagittal_image)) = [];
3961 
+      order = [order; nii_view.handles.sagittal_image];
3962 
+
3963 
+      if isfield(nii_view.handles,'sagittal_bg') & ~isempty(nii_view.handles.sagittal_bg)
3964 
+         order(find(order == nii_view.handles.sagittal_bg)) = [];
3965 
+         order = [order; nii_view.handles.sagittal_bg];
3966 
+      end
3967 
+
3968 
+      set(gca, 'child', order);
3969 
+
3970 
+      if ~useinterp
3971 
+         if isfield(nii_view.handles,'sagittal_bg') & ~isempty(nii_view.handles.sagittal_bg)
3972 
+            delete(nii_view.handles.sagittal_bg);
3973 
+            nii_view.handles.sagittal_bg = [];
3974 
+         end
3975 
+      end
3976 
+
3977 
+      set(nii_view.handles.sagittal_image,'buttondown','view_nii(''sagittal_image'');');
3978 
+   end
3979 
+
3980 
+   if ~useinterp
3981 
+      nii_view.bgimg = [];
3982 
+   end
3983 
+
3984 
+   set_coordinates(nii_view,useinterp);
3985 
+   setappdata(fig, 'nii_view', nii_view);
3986 
+
3987 
+   return;					% update_useinterp
3988 
+
3989 
+
3990 
+%----------------------------------------------------------------
3991 
+function update_useimagesc(fig, useimagesc)
3992 
+
3993 
+   if isempty(useimagesc)
3994 
+      return;
3995 
+   end
3996 
+
3997 
+   if useimagesc
3998 
+      v='scaled';
3999 
+   else
4000 
+      v='direct';
4001 
+   end
4002 
+
4003 
+   nii_view = getappdata(fig,'nii_view');
4004 
+   handles = nii_view.handles;
4005 
+
4006 
+   if isfield(handles,'cbar_image') & ishandle(handles.cbar_image)
4007 
+%      set(handles.cbar_image,'cdatamapping',v);
4008 
+   end
4009 
+
4010 
+   set(handles.axial_image,'cdatamapping',v);
4011 
+   set(handles.coronal_image,'cdatamapping',v);
4012 
+   set(handles.sagittal_image,'cdatamapping',v);
4013 
+
4014 
+   return;					% update_useimagesc
4015 
+
4016 
+
4017 
+%----------------------------------------------------------------
4018 
+function update_shape(fig, area, usecolorbar, usestretch, useimagesc)
4019 
+
4020 
+   nii_view = getappdata(fig,'nii_view');
4021 
+
4022 
+   if isempty(usestretch)		% no change, get usestretch
4023 
+      stretchchange = 0;
4024 
+      usestretch = nii_view.usestretch;
4025 
+   else					% change, set usestretch
4026 
+      stretchchange = 1;
4027 
+      nii_view.usestretch = usestretch;
4028 
+   end
4029 
+
4030 
+   if isempty(area)			% no change, get area
4031 
+
4032 
+      areachange = 0;
4033 
+      area = nii_view.area;
4034 
+
4035 
+   elseif ~isempty(nii_view.cbar_area)	% change, set area & cbar_area
4036 
+
4037 
+      areachange = 1;
4038 
+      cbar_area = area;
4039 
+      cbar_area(1) = area(1) + area(3)*0.93;
4040 
+      cbar_area(3) = area(3)*0.04;
4041 
+      area(3) = area(3)*0.9;		% 90% used for main axes
4042 
+
4043 
+      [cbar_axes cbarminmax_axes] = create_cbar_axes(fig, cbar_area);
4044 
+
4045 
+      nii_view.area = area;
4046 
+      nii_view.cbar_area = cbar_area;
4047 
+
4048 
+   else					% change, set area only
4049 
+      areachange = 1;
4050 
+      nii_view.area = area;
4051 
+   end
4052 
+
4053 
+   %  Add colorbar
4054 
+   %
4055 
+   if ~isempty(usecolorbar) & usecolorbar & isempty(nii_view.cbar_area)
4056 
+
4057 
+      colorbarchange = 1;
4058 
+
4059 
+      cbar_area = area;
4060 
+      cbar_area(1) = area(1) + area(3)*0.93;
4061 
+      cbar_area(3) = area(3)*0.04;
4062 
+      area(3) = area(3)*0.9;		% 90% used for main axes
4063 
+
4064 
+      %  create axes for colorbar
4065 
+      %
4066 
+      [cbar_axes cbarminmax_axes] = create_cbar_axes(fig, cbar_area);
4067 
+
4068 
+      nii_view.area = area;
4069 
+      nii_view.cbar_area = cbar_area;
4070 
+
4071 
+      %  useimagesc follows axial image
4072 
+      %
4073 
+      if isempty(useimagesc)
4074 
+         if strcmpi(get(nii_view.handles.axial_image,'cdatamap'),'scaled')
4075 
+            useimagesc = 1;
4076 
+         else
4077 
+            useimagesc = 0;
4078 
+         end
4079 
+      end
4080 
+
4081 
+      if isfield(nii_view, 'highcolor') & ~isempty(highcolor)
4082 
+         num_highcolor = size(nii_view.highcolor,1);
4083 
+      else
4084 
+         num_highcolor = 0;
4085 
+      end
4086 
+
4087 
+      if isfield(nii_view, 'colorlevel') & ~isempty(nii_view.colorlevel)
4088 
+         colorlevel = nii_view.colorlevel;
4089 
+      else
4090 
+         colorlevel = 256 - num_highcolor;
4091 
+      end
4092 
+
4093 
+      if isfield(nii_view, 'color_map')
4094 
+         color_map = nii_view.color_map;
4095 
+      else
4096 
+         color_map = [];
4097 
+      end
4098 
+
4099 
+      if isfield(nii_view, 'highcolor')
4100 
+         highcolor = nii_view.highcolor;
4101 
+      else
4102 
+         highcolor = [];
4103 
+      end
4104 
+
4105 
+      %  plot colorbar
4106 
+      %
4107 
+if 0
4108 
+      if isempty(color_map)
4109 
+         level = colorlevel + num_highcolor;
4110 
+      else
4111 
+         level = size([color_map; highcolor], 1);
4112 
+      end
4113 
+end
4114 
+
4115 
+      if isempty(color_map)
4116 
+         level = colorlevel;
4117 
+      else
4118 
+         level = size([color_map], 1);
4119 
+      end
4120 
+
4121 
+      cbar_image = [1:level]';
4122 
+
4123 
+      niiclass = class(nii_view.nii.img);
4124 
+
4125 
+      h1 = plot_cbar(fig, cbar_axes, cbarminmax_axes, nii_view.cbarminmax, ...
4126 
+		level, nii_view.handles, useimagesc, nii_view.colorindex, ...
4127 
+		color_map, colorlevel, highcolor, niiclass, nii_view.numscan);
4128 
+      nii_view.handles.cbar_image = h1;
4129 
+      nii_view.handles.cbar_axes = cbar_axes;
4130 
+      nii_view.handles.cbarminmax_axes = cbar_axes;
4131 
+
4132 
+   %  remove colorbar
4133 
+   %
4134 
+   elseif ~isempty(usecolorbar) & ~usecolorbar & ~isempty(nii_view.cbar_area)
4135 
+
4136 
+      colorbarchange = 1;
4137 
+
4138 
+      area(3) = area(3) / 0.9;
4139 
+
4140 
+      nii_view.area = area;
4141 
+      nii_view.cbar_area = [];
4142 
+
4143 
+      nii_view.handles = rmfield(nii_view.handles,'cbar_image');
4144 
+      delete(nii_view.handles.cbarminmax_axes);
4145 
+      nii_view.handles = rmfield(nii_view.handles,'cbarminmax_axes');
4146 
+      delete(nii_view.handles.cbar_axes);
4147 
+      nii_view.handles = rmfield(nii_view.handles,'cbar_axes');
4148 
+
4149 
+   else
4150 
+      colorbarchange = 0;
4151 
+   end
4152 
+
4153 
+   if colorbarchange | stretchchange | areachange
4154 
+      setappdata(fig,'nii_view',nii_view);
4155 
+      update_usestretch(fig, usestretch);
4156 
+   end
4157 
+
4158 
+   return;					% update_shape
4159 
+
4160 
+
4161 
+%----------------------------------------------------------------
4162 
+function update_unit(fig, setunit)
4163 
+
4164 
+   if isempty(setunit)
4165 
+      return;
4166 
+   end
4167 
+
4168 
+   if strcmpi(setunit,'mm') | strcmpi(setunit,'millimeter') | strcmpi(setunit,'mni')
4169 
+      v = 2;
4170 
+%   elseif strcmpi(setunit,'tal') | strcmpi(setunit,'talairach')
4171 
+ %     v = 3;
4172 
+   elseif strcmpi(setunit,'vox') | strcmpi(setunit,'voxel')
4173 
+      v = 1;
4174 
+   else
4175 
+      v = 1;
4176 
+   end
4177 
+
4178 
+   nii_view = getappdata(fig,'nii_view');
4179 
+   set(nii_view.handles.coord, 'value', v);
4180 
+   set_image_value(nii_view);
4181 
+
4182 
+   return;					% update_unit
4183 
+
4184 
+
4185 
+%----------------------------------------------------------------
4186 
+function update_viewpoint(fig, setviewpoint)
4187 
+
4188 
+   if isempty(setviewpoint)
4189 
+      return;
4190 
+   end
4191 
+
4192 
+   nii_view = getappdata(fig,'nii_view');
4193 
+
4194 
+   if length(setviewpoint) ~= 3
4195 
+      error('Viewpoint position should contain [x y z]');
4196 
+   end
4197 
+
4198 
+   set(nii_view.handles.impos,'string',num2str(setviewpoint));
4199 
+
4200 
+   opt.command = 'impos_edit';
4201 
+   view_nii(fig, opt);
4202 
+
4203 
+   set(nii_view.handles.axial_axes,'selected','on');
4204 
+   set(nii_view.handles.axial_axes,'selected','off');
4205 
+   set(nii_view.handles.coronal_axes,'selected','on');
4206 
+   set(nii_view.handles.coronal_axes,'selected','off');
4207 
+   set(nii_view.handles.sagittal_axes,'selected','on');
4208 
+   set(nii_view.handles.sagittal_axes,'selected','off');
4209 
+
4210 
+   return;					% update_viewpoint
4211 
+
4212 
+
4213 
+%----------------------------------------------------------------
4214 
+function update_scanid(fig, setscanid)
4215 
+
4216 
+   if isempty(setscanid)
4217 
+      return;
4218 
+   end
4219 
+
4220 
+   nii_view = getappdata(fig,'nii_view');
4221 
+
4222 
+   if setscanid < 1
4223 
+      setscanid = 1;
4224 
+   end
4225 
+
4226 
+   if setscanid > nii_view.numscan
4227 
+      setscanid = nii_view.numscan;
4228 
+   end
4229 
+
4230 
+   set(nii_view.handles.contrast_def,'string',num2str(setscanid));
4231 
+   set(nii_view.handles.contrast,'value',setscanid);
4232 
+
4233 
+   opt.command = 'updateimg';
4234 
+   opt.setscanid = setscanid;
4235 
+
4236 
+   view_nii(fig, nii_view.nii.img, opt);
4237 
+
4238 
+   return;					% update_scanid
4239 
+
4240 
+
4241 
+%----------------------------------------------------------------
4242 
+function update_crosshaircolor(fig, new_color)
4243 
+
4244 
+   if isempty(new_color)
4245 
+      return;
4246 
+   end
4247 
+
4248 
+   nii_view = getappdata(fig,'nii_view');
4249 
+   xhair_color = nii_view.handles.xhair_color;
4250 
+
4251 
+   set(xhair_color,'user',new_color);
4252 
+   set(nii_view.axi_xhair.lx,'color',new_color);
4253 
+   set(nii_view.axi_xhair.ly,'color',new_color);
4254 
+   set(nii_view.cor_xhair.lx,'color',new_color);
4255 
+   set(nii_view.cor_xhair.ly,'color',new_color);
4256 
+   set(nii_view.sag_xhair.lx,'color',new_color);
4257 
+   set(nii_view.sag_xhair.ly,'color',new_color);
4258 
+
4259 
+   return;					% update_crosshaircolor
4260 
+
4261 
+
4262 
+%----------------------------------------------------------------
4263 
+function update_colorindex(fig, colorindex)
4264 
+
4265 
+   if isempty(colorindex)
4266 
+      return;
4267 
+   end
4268 
+
4269 
+   nii_view = getappdata(fig,'nii_view');
4270 
+   nii_view.colorindex = colorindex;
4271 
+   setappdata(fig, 'nii_view', nii_view);
4272 
+   set(nii_view.handles.colorindex,'value',colorindex);
4273 
+
4274 
+   opt.command = 'color';
4275 
+   view_nii(fig, opt);
4276 
+
4277 
+   return;					% update_colorindex
4278 
+
4279 
+
4280 
+%----------------------------------------------------------------
4281 
+function redraw_cbar(fig, colorlevel, color_map, highcolor)
4282 
+
4283 
+   nii_view = getappdata(fig,'nii_view');
4284 
+
4285 
+   if isempty(nii_view.cbar_area)
4286 
+      return;
4287 
+   end
4288 
+
4289 
+   colorindex = nii_view.colorindex;
4290 
+
4291 
+   if isempty(highcolor)
4292 
+      num_highcolor = 0;
4293 
+   else
4294 
+      num_highcolor = size(highcolor,1);
4295 
+   end
4296 
+
4297 
+   if isempty(colorlevel)
4298 
+      colorlevel=256;
4299 
+   end
4300 
+
4301 
+   if colorindex == 1
4302 
+      colorlevel = size(color_map, 1);
4303 
+   end
4304 
+
4305 
+%   level = colorlevel + num_highcolor;
4306 
+   level = colorlevel;
4307 
+
4308 
+   cbar_image = [1:level]';
4309 
+
4310 
+   cbar_area = nii_view.cbar_area;
4311 
+
4312 
+   %  useimagesc follows axial image
4313 
+   %
4314 
+   if strcmpi(get(nii_view.handles.axial_image,'cdatamap'),'scaled')
4315 
+      useimagesc = 1;
4316 
+   else
4317 
+      useimagesc = 0;
4318 
+   end
4319 
+
4320 
+   niiclass = class(nii_view.nii.img);
4321 
+
4322 
+   delete(nii_view.handles.cbar_image);
4323 
+   delete(nii_view.handles.cbar_axes);
4324 
+   delete(nii_view.handles.cbarminmax_axes);
4325 
+
4326 
+   [nii_view.handles.cbar_axes nii_view.handles.cbarminmax_axes] = ...
4327 
+	create_cbar_axes(fig, cbar_area, []);
4328 
+
4329 
+   nii_view.handles.cbar_image = plot_cbar(fig, ...
4330 
+	nii_view.handles.cbar_axes, nii_view.handles.cbarminmax_axes, ...
4331 
+	nii_view.cbarminmax, level, nii_view.handles, useimagesc, ...
4332 
+	colorindex, color_map, colorlevel, highcolor, niiclass, ...
4333 
+	nii_view.numscan, []);
4334 
+
4335 
+   setappdata(fig, 'nii_view', nii_view);
4336 
+
4337 
+   return;					% redraw_cbar
4338 
+
4339 
+
4340 
+%----------------------------------------------------------------
4341 
+function update_buttondown(fig, setbuttondown)
4342 
+
4343 
+   if isempty(setbuttondown)
4344 
+      return;
4345 
+   end
4346 
+
4347 
+   nii_view = getappdata(fig,'nii_view');
4348 
+   nii_view.buttondown = setbuttondown;
4349 
+   setappdata(fig, 'nii_view', nii_view);
4350 
+
4351 
+   return;					% update_buttondown
4352 
+
4353 
+
4354 
+%----------------------------------------------------------------
4355 
+function update_cbarminmax(fig, cbarminmax)
4356 
+
4357 
+   if isempty(cbarminmax)
4358 
+      return;
4359 
+   end
4360 
+
4361 
+   nii_view = getappdata(fig, 'nii_view');
4362 
+
4363 
+   if ~isfield(nii_view.handles, 'cbarminmax_axes')
4364 
+      return;
4365 
+   end
4366 
+
4367 
+   nii_view.cbarminmax = cbarminmax;
4368 
+   setappdata(fig, 'nii_view', nii_view);
4369 
+
4370 
+   axes(nii_view.handles.cbarminmax_axes);
4371 
+
4372 
+   plot([0 0], cbarminmax, 'w');
4373 
+   axis tight;
4374 
+
4375 
+   set(nii_view.handles.cbarminmax_axes,'YDir','normal', ...
4376 
+      'XLimMode','manual','YLimMode','manual','YColor',[0 0 0], ...
4377 
+      'XColor',[0 0 0],'xtick',[],'YAxisLocation','right');
4378 
+
4379 
+   ylim = get(nii_view.handles.cbar_axes,'ylim');
4380 
+   ylimb = get(nii_view.handles.cbarminmax_axes,'ylim');
4381 
+   ytickb = get(nii_view.handles.cbarminmax_axes,'ytick');
4382 
+   ytick=(ylim(2)-ylim(1))*(ytickb-ylimb(1))/(ylimb(2)-ylimb(1))+ylim(1);
4383 
+
4384 
+   axes(nii_view.handles.cbar_axes);
4385 
+
4386 
+   set(nii_view.handles.cbar_axes,'YDir','normal','XLimMode','manual', ...
4387 
+	'YLimMode','manual','YColor',[0 0 0],'XColor',[0 0 0],'xtick',[], ...
4388 
+	'YAxisLocation','right','ylim',ylim,'ytick',ytick,'yticklabel','');
4389 
+
4390 
+   return;					% update_cbarminmax
4391 
+
4392 
+
4393 
+%----------------------------------------------------------------
4394 
+function update_highcolor(fig, highcolor, colorlevel)
4395 
+
4396 
+   nii_view = getappdata(fig,'nii_view');
4397 
+
4398 
+   if ischar(highcolor) & (isempty(colorlevel) | nii_view.colorindex == 1)
4399 
+      return;
4400 
+   end
4401 
+
4402 
+   if ~ischar(highcolor)
4403 
+      nii_view.highcolor = highcolor;
4404 
+
4405 
+      if isempty(highcolor)
4406 
+         nii_view = rmfield(nii_view, 'highcolor');
4407 
+      end
4408 
+   else
4409 
+      highcolor = [];
4410 
+   end
4411 
+
4412 
+   if isempty(colorlevel) | nii_view.colorindex == 1
4413 
+      nii_view.colorlevel = nii_view.colorlevel - size(highcolor,1);
4414 
+   else
4415 
+      nii_view.colorlevel = colorlevel;
4416 
+   end
4417 
+
4418 
+   setappdata(fig, 'nii_view', nii_view);
4419 
+
4420 
+   if isfield(nii_view,'color_map')
4421 
+      color_map = nii_view.color_map;
4422 
+   else
4423 
+      color_map = [];
4424 
+   end
4425 
+
4426 
+   redraw_cbar(fig, nii_view.colorlevel, color_map, highcolor);
4427 
+   change_colormap(fig);
4428 
+
4429 
+   return;					% update_highcolor
4430 
+
4431 
+
4432 
+%----------------------------------------------------------------
4433 
+function update_colormap(fig, color_map)
4434 
+
4435 
+   if ischar(color_map)
4436 
+      return;
4437 
+   end
4438 
+
4439 
+   nii_view = getappdata(fig,'nii_view');
4440 
+   nii = nii_view.nii;
4441 
+   minvalue = nii_view.minvalue;
4442 
+
4443 
+   if isempty(color_map)
4444 
+      if minvalue < 0
4445 
+         colorindex = 2;
4446 
+      else
4447 
+         colorindex = 3;
4448 
+      end
4449 
+
4450 
+      nii_view = rmfield(nii_view, 'color_map');
4451 
+      setappdata(fig,'nii_view',nii_view);
4452 
+      update_colorindex(fig, colorindex);
4453 
+      return;
4454 
+   else
4455 
+      colorindex = 1;
4456 
+      nii_view.color_map = color_map;
4457 
+      nii_view.colorindex = colorindex;
4458 
+      setappdata(fig,'nii_view',nii_view);
4459 
+      set(nii_view.handles.colorindex,'value',colorindex);
4460 
+   end
4461 
+
4462 
+   colorlevel = nii_view.colorlevel;
4463 
+
4464 
+   if isfield(nii_view, 'highcolor')
4465 
+      highcolor = nii_view.highcolor;
4466 
+   else
4467 
+      highcolor = [];
4468 
+   end
4469 
+
4470 
+   redraw_cbar(fig, colorlevel, color_map, highcolor);
4471 
+   change_colormap(fig);
4472 
+
4473 
+   opt.enablecontrast = 0;
4474 
+   update_enable(fig, opt);
4475 
+
4476 
+   return;					% update_colormap
4477 
+
4478 
+
4479 
+%----------------------------------------------------------------
4480 
+function status = get_status(h);
4481 
+
4482 
+   nii_view = getappdata(h,'nii_view');
4483 
+
4484 
+   status.fig = h;
4485 
+   status.area = nii_view.area;
4486 
+
4487 
+   if isempty(nii_view.cbar_area)
4488 
+      status.usecolorbar = 0;
4489 
+   else
4490 
+      status.usecolorbar = 1;
4491 
+      width = status.area(3) / 0.9;
4492 
+      status.area(3) = width;
4493 
+   end
4494 
+
4495 
+   if strcmpi(get(nii_view.handles.imval,'visible'), 'on')
4496 
+      status.usepanel = 1;
4497 
+   else
4498 
+      status.usepanel = 0;
4499 
+   end
4500 
+
4501 
+   if get(nii_view.handles.xhair,'value') == 1
4502 
+      status.usecrosshair = 1;
4503 
+   else
4504 
+      status.usecrosshair = 0;
4505 
+   end
4506 
+
4507 
+   status.usestretch = nii_view.usestretch;
4508 
+
4509 
+   if strcmpi(get(nii_view.handles.axial_image,'cdatamapping'), 'direct')
4510 
+      status.useimagesc = 0;
4511 
+   else
4512 
+      status.useimagesc = 1;
4513 
+   end
4514 
+
4515 
+   status.useinterp = nii_view.useinterp;
4516 
+
4517 
+   if get(nii_view.handles.coord,'value') == 1
4518 
+      status.unit = 'vox';
4519 
+   elseif get(nii_view.handles.coord,'value') == 2
4520 
+      status.unit = 'mm';
4521 
+   elseif get(nii_view.handles.coord,'value') == 3
4522 
+      status.unit = 'tal';
4523 
+   end
4524 
+
4525 
+   status.viewpoint = get(nii_view.handles.impos,'value');
4526 
+   status.scanid = nii_view.scanid;
4527 
+   status.intensity = get(nii_view.handles.imval,'value');
4528 
+   status.colorindex = get(nii_view.handles.colorindex,'value');
4529 
+
4530 
+   if isfield(nii_view,'color_map')
4531 
+      status.colormap = nii_view.color_map;
4532 
+   else
4533 
+      status.colormap = [];
4534 
+   end
4535 
+
4536 
+   status.colorlevel = nii_view.colorlevel;
4537 
+
4538 
+   if isfield(nii_view,'highcolor')
4539 
+      status.highcolor = nii_view.highcolor;
4540 
+   else
4541 
+      status.highcolor = [];
4542 
+   end
4543 
+
4544 
+   status.cbarminmax = nii_view.cbarminmax;
4545 
+   status.buttondown = nii_view.buttondown;
4546 
+
4547 
+   return;					% get_status
4548 
+
4549 
+
4550 
+%----------------------------------------------------------------
4551 
+function [custom_color_map, colorindex] ...
4552 
+		 = change_colormap(fig, nii, colorindex, cbarminmax)
4553 
+
4554 
+   custom_color_map = [];
4555 
+
4556 
+   if ~exist('nii', 'var')
4557 
+      nii_view = getappdata(fig,'nii_view');
4558 
+   else
4559 
+      nii_view = nii;
4560 
+   end
4561 
+
4562 
+   if ~exist('colorindex', 'var')
4563 
+      colorindex = get(nii_view.handles.colorindex,'value');
4564 
+   end
4565 
+
4566 
+   if ~exist('cbarminmax', 'var')
4567 
+      cbarminmax = nii_view.cbarminmax;
4568 
+   end
4569 
+
4570 
+   if isfield(nii_view, 'highcolor') & ~isempty(nii_view.highcolor)
4571 
+      highcolor = nii_view.highcolor;
4572 
+      num_highcolor = size(highcolor,1);
4573 
+   else
4574 
+      highcolor = [];
4575 
+      num_highcolor = 0;
4576 
+   end
4577 
+
4578 
+%   if isfield(nii_view, 'colorlevel') & ~isempty(nii_view.colorlevel)
4579 
+   if nii_view.colorlevel < 256
4580 
+      num_color = nii_view.colorlevel;
4581 
+   else
4582 
+      num_color = 256 - num_highcolor;
4583 
+   end
4584 
+
4585 
+   contrast = [];
4586 
+
4587 
+   if colorindex == 3					% for gray
4588 
+      if nii_view.numscan > 1
4589 
+         contrast = 1;
4590 
+      else
4591 
+         contrast = (num_color-1)*(get(nii_view.handles.contrast,'value')-1)/255+1;
4592 
+         contrast = floor(contrast);
4593 
+      end
4594 
+   elseif colorindex == 2				% for bipolar
4595 
+      if nii_view.numscan > 1
4596 
+         contrast = 128;
4597 
+      else
4598 
+         contrast = get(nii_view.handles.contrast,'value');
4599 
+      end
4600 
+   end
4601 
+
4602 
+   if isfield(nii_view,'color_map') & ~isempty(nii_view.color_map)
4603 
+      color_map = nii_view.color_map;
4604 
+      custom_color_map = color_map;
4605 
+   elseif colorindex == 1
4606 
+      [f p] = uigetfile('*.txt', 'Input colormap text file');
4607 
+
4608 
+      if p==0
4609 
+         colorindex = nii_view.colorindex;
4610 
+         set(nii_view.handles.colorindex,'value',colorindex);
4611 
+         return;
4612 
+      end;
4613 
+
4614 
+      try
4615 
+         custom_color_map = load(fullfile(p,f));
4616 
+         loadfail = 0;
4617 
+      catch
4618 
+         loadfail = 1;
4619 
+      end
4620 
+
4621 
+      if loadfail | isempty(custom_color_map) | size(custom_color_map,2)~=3 ...
4622 
+	| min(custom_color_map(:)) < 0 | max(custom_color_map(:)) > 1
4623 
+
4624 
+         msg = 'Colormap should be a Mx3 matrix with value between 0 and 1';
4625 
+         msgbox(msg,'Error in colormap file');
4626 
+         colorindex = nii_view.colorindex;
4627 
+         set(nii_view.handles.colorindex,'value',colorindex);
4628 
+         return;
4629 
+      end
4630 
+
4631 
+      color_map = custom_color_map;
4632 
+      nii_view.color_map = color_map;
4633 
+   end
4634 
+
4635 
+   switch colorindex
4636 
+   case {2}
4637 
+      color_map = bipolar(num_color, cbarminmax(1), cbarminmax(2), contrast);
4638 
+   case {3}
4639 
+      color_map = gray(num_color - contrast + 1);
4640 
+   case {4}
4641 
+      color_map = jet(num_color);
4642 
+   case {5}
4643 
+      color_map = cool(num_color);
4644 
+   case {6}
4645 
+      color_map = bone(num_color);
4646 
+   case {7}
4647 
+      color_map = hot(num_color);
4648 
+   case {8}
4649 
+      color_map = copper(num_color);
4650 
+   case {9}
4651 
+      color_map = pink(num_color);
4652 
+   end
4653 
+
4654 
+   nii_view.colorindex = colorindex;
4655 
+
4656 
+   if ~exist('nii', 'var')
4657 
+      setappdata(fig,'nii_view',nii_view);
4658 
+   end
4659 
+
4660 
+   if colorindex == 3
4661 
+      color_map = [zeros(contrast,3); color_map(2:end,:)];
4662 
+   end
4663 
+
4664 
+   if get(nii_view.handles.neg_color,'value') & isempty(highcolor)
4665 
+      color_map = flipud(color_map);
4666 
+   elseif get(nii_view.handles.neg_color,'value') & ~isempty(highcolor)
4667 
+      highcolor = flipud(highcolor);
4668 
+   end
4669 
+
4670 
+   brightness = get(nii_view.handles.brightness,'value');
4671 
+   color_map = brighten(color_map, brightness);
4672 
+
4673 
+   color_map = [color_map; highcolor];
4674 
+
4675 
+   set(fig, 'colormap', color_map);
4676 
+
4677 
+   return;					% change_colormap
4678 
+
4679 
+
4680 
+%----------------------------------------------------------------
4681 
+function move_cursor(fig)
4682 
+
4683 
+   nii_view = getappdata(fig, 'nii_view');
4684 
+
4685 
+   if isempty(nii_view)
4686 
+      return;
4687 
+   end
4688 
+
4689 
+   axi = get(nii_view.handles.axial_axes, 'pos');
4690 
+   cor = get(nii_view.handles.coronal_axes, 'pos');
4691 
+   sag = get(nii_view.handles.sagittal_axes, 'pos');
4692 
+   curr = get(fig, 'currentpoint');
4693 
+
4694 
+   if		curr(1) >= axi(1) & curr(1) <= axi(1)+axi(3) & ...
4695 
+		curr(2) >= axi(2) & curr(2) <= axi(2)+axi(4)
4696 
+
4697 
+      curr = get(nii_view.handles.axial_axes, 'current');
4698 
+      sag = curr(1,1);
4699 
+      cor = curr(1,2);
4700 
+      axi = nii_view.slices.axi;
4701 
+
4702 
+   elseif	curr(1) >= cor(1) & curr(1) <= cor(1)+cor(3) & ...
4703 
+		curr(2) >= cor(2) & curr(2) <= cor(2)+cor(4)
4704 
+
4705 
+      curr = get(nii_view.handles.coronal_axes, 'current');
4706 
+      sag = curr(1,1);
4707 
+      cor = nii_view.slices.cor;
4708 
+      axi = curr(1,2);
4709 
+
4710 
+   elseif	curr(1) >= sag(1) & curr(1) <= sag(1)+sag(3) & ...
4711 
+		curr(2) >= sag(2) & curr(2) <= sag(2)+sag(4)
4712 
+
4713 
+      curr = get(nii_view.handles.sagittal_axes, 'current');
4714 
+
4715 
+      sag = nii_view.slices.sag;
4716 
+      cor = curr(1,1);
4717 
+      axi = curr(1,2);
4718 
+
4719 
+   else
4720 
+
4721 
+      set(nii_view.handles.imvalcur,'String',' ');
4722 
+      set(nii_view.handles.imposcur,'String',' ');
4723 
+      return;
4724 
+
4725 
+   end
4726 
+
4727 
+    sag = round(sag);
4728 
+    cor = round(cor);
4729 
+    axi = round(axi);
4730 
+
4731 
+    if sag < 1
4732 
+       sag = 1;
4733 
+    elseif sag > nii_view.dims(1)
4734 
+       sag = nii_view.dims(1);
4735 
+    end
4736 
+
4737 
+    if cor < 1
4738 
+       cor = 1;
4739 
+    elseif cor > nii_view.dims(2)
4740 
+       cor = nii_view.dims(2);
4741 
+    end
4742 
+
4743 
+    if axi < 1
4744 
+       axi = 1;
4745 
+    elseif axi > nii_view.dims(3)
4746 
+       axi = nii_view.dims(3);
4747 
+    end
4748 
+
4749 
+    if 0 % isfield(nii_view, 'disp')
4750 
+       img = nii_view.disp;
4751 
+    else
4752 
+       img = nii_view.nii.img;
4753 
+    end
4754 
+
4755 
+    if nii_view.nii.hdr.dime.datatype == 128
4756 
+       imgvalue = [double(img(sag,cor,axi,1,nii_view.scanid)) double(img(sag,cor,axi,2,nii_view.scanid)) double(img(sag,cor,axi,3,nii_view.scanid))];
4757 
+       set(nii_view.handles.imvalcur,'String',sprintf('%7.4g %7.4g %7.4g',imgvalue));
4758 
+    elseif nii_view.nii.hdr.dime.datatype == 511
4759 
+       R = double(img(sag,cor,axi,1,nii_view.scanid)) * (nii_view.nii.hdr.dime.glmax - ...
4760 
+		nii_view.nii.hdr.dime.glmin) + nii_view.nii.hdr.dime.glmin;
4761 
+       G = double(img(sag,cor,axi,2,nii_view.scanid)) * (nii_view.nii.hdr.dime.glmax - ...
4762 
+		nii_view.nii.hdr.dime.glmin) + nii_view.nii.hdr.dime.glmin;
4763 
+       B = double(img(sag,cor,axi,3,nii_view.scanid)) * (nii_view.nii.hdr.dime.glmax - ...
4764 
+		nii_view.nii.hdr.dime.glmin) + nii_view.nii.hdr.dime.glmin;
4765 
+       imgvalue = [R G B];
4766 
+       set(nii_view.handles.imvalcur,'String',sprintf('%7.4g %7.4g %7.4g',imgvalue));
4767 
+    else
4768 
+       imgvalue = double(img(sag,cor,axi,nii_view.scanid));
4769 
+
4770 
+       if isnan(imgvalue) | imgvalue > nii_view.cbarminmax(2)
4771 
+          imgvalue = 0;
4772 
+       end
4773 
+
4774 
+       set(nii_view.handles.imvalcur,'String',sprintf('%.6g',imgvalue));
4775 
+    end
4776 
+
4777 
+    nii_view.slices.sag = sag;
4778 
+    nii_view.slices.cor = cor;
4779 
+    nii_view.slices.axi = axi;
4780 
+
4781 
+    nii_view = update_imgXYZ(nii_view);
4782 
+
4783 
+    if get(nii_view.handles.coord,'value') == 1,
4784 
+       sag = nii_view.imgXYZ.vox(1);
4785 
+       cor = nii_view.imgXYZ.vox(2);
4786 
+       axi = nii_view.imgXYZ.vox(3);
4787 
+    elseif get(nii_view.handles.coord,'value') == 2,
4788 
+       sag = nii_view.imgXYZ.mm(1);
4789 
+       cor = nii_view.imgXYZ.mm(2);
4790 
+       axi = nii_view.imgXYZ.mm(3);
4791 
+    elseif get(nii_view.handles.coord,'value') == 3,
4792 
+       sag = nii_view.imgXYZ.tal(1);
4793 
+       cor = nii_view.imgXYZ.tal(2);
4794 
+       axi = nii_view.imgXYZ.tal(3);
4795 
+    end
4796 
+
4797 
+    if get(nii_view.handles.coord,'value') == 1,
4798 
+        string = sprintf('%7.0f %7.0f %7.0f',sag,cor,axi);
4799 
+    else
4800 
+        string = sprintf('%7.1f %7.1f %7.1f',sag,cor,axi);
4801 
+    end;
4802 
+
4803 
+    set(nii_view.handles.imposcur,'String',string);
4804 
+
4805 
+    return;					% move_cursor
4806 
+
4807 
+
4808 
+%----------------------------------------------------------------
4809 
+function change_scan(hdl_str)
4810 
+
4811 
+   fig = gcbf;
4812 
+   nii_view = getappdata(fig,'nii_view');
4813 
+
4814 
+   if strcmpi(hdl_str, 'edit_change_scan')		% edit
4815 
+      hdl = nii_view.handles.contrast_def;
4816 
+      setscanid = round(str2num(get(hdl, 'string')));
4817 
+   else							% slider
4818 
+      hdl = nii_view.handles.contrast;
4819 
+      setscanid = round(get(hdl, 'value'));
4820 
+   end
4821 
+
4822 
+   update_scanid(fig, setscanid);
4823 
+
4824 
+   return;					% change_scan
4825 
+
4826 
+
4827 
+%----------------------------------------------------------------
4828 
+function val = scale_in(val, minval, maxval, range)
4829 
+
4830 
+   %  scale value into range
4831 
+   %
4832 
+   val = range*(double(val)-double(minval))/(double(maxval)-double(minval))+1;
4833 
+
4834 
+   return;					% scale_in
4835 
+
4836 
+
4837 
+%----------------------------------------------------------------
4838 
+function val = scale_out(val, minval, maxval, range)
4839 
+
4840 
+   %  according to [minval maxval] and range of color levels (e.g. 199)
4841 
+   %  scale val back from any thing between 1~256 to a small number that
4842 
+   %  is corresonding to [minval maxval].
4843 
+   %
4844 
+   val = (double(val)-1)*(double(maxval)-double(minval))/range+double(minval);
4845 
+
4846 
+   return;					% scale_out
4847 
+
NIFTI_20090325/view_nii_menu.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,317 @@
1 
+%  Imbed Zoom, Interp, and Info menu to view_nii window.
2 
+%
3 
+%  Usage: view_nii_menu(fig);
4 
+%
5 
+
6 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
7 
+%
8 
+%--------------------------------------------------------------------
9 
+function menu_hdl = view_nii_menu(fig, varargin)
10 
+
11 
+   if isnumeric(fig)
12 
+      menu_hdl = init(fig);
13 
+      return;
14 
+   end
15 
+
16 
+   menu_hdl = [];
17 
+
18 
+   switch fig
19 
+   case 'interp'
20 
+      if nargin > 1
21 
+         fig = varargin{1};
22 
+      else
23 
+         fig = gcbf;
24 
+      end
25 
+
26 
+      nii_menu = getappdata(fig, 'nii_menu');
27 
+      interp_on_state = get(nii_menu.Minterp,'Userdata');
28 
+
29 
+      if (interp_on_state == 1)
30 
+         opt.useinterp = 1;
31 
+         view_nii(fig,opt);
32 
+         set(nii_menu.Minterp,'Userdata',0,'Label','Interp off');
33 
+         reset_zoom(fig);
34 
+      else
35 
+         opt.useinterp = 0;
36 
+         view_nii(fig,opt);
37 
+         set(nii_menu.Minterp,'Userdata',1,'Label','Interp on');
38 
+         reset_zoom(fig);
39 
+      end
40 
+   case 'reset_zoom'
41 
+      if nargin > 1
42 
+         fig = varargin{1};
43 
+      else
44 
+         fig = gcbf;
45 
+      end
46 
+
47 
+      reset_zoom(fig);
48 
+   case 'orient'
49 
+      orient;
50 
+   case 'img_info'
51 
+      img_info;
52 
+   case 'save_disp'
53 
+      save_disp;
54 
+   end
55 
+
56 
+   return					% view_nii_menu
57 
+
58 
+
59 
+%--------------------------------------------------------------------
60 
+function menu_hdl = init(fig)
61 
+
62 
+   %  search for edit, view menu
63 
+   %
64 
+   nii_menu.Mfile = [];
65 
+   nii_menu.Medit = [];
66 
+   nii_menu.Mview = [];
67 
+   menuitems = findobj(fig, 'type', 'uimenu');
68 
+
69 
+   for i=1:length(menuitems)
70 
+      filelabel = get(menuitems(i),'label');
71 
+
72 
+      if strcmpi(strrep(filelabel, '&', ''), 'file')
73 
+         nii_menu.Mfile = menuitems(i);
74 
+      end
75 
+
76 
+      editlabel = get(menuitems(i),'label');
77 
+
78 
+      if strcmpi(strrep(editlabel, '&', ''), 'edit')
79 
+         nii_menu.Medit = menuitems(i);
80 
+      end
81 
+
82 
+      viewlabel = get(menuitems(i),'label');
83 
+
84 
+      if strcmpi(strrep(viewlabel, '&', ''), 'view')
85 
+         nii_menu.Mview = menuitems(i);
86 
+      end
87 
+   end
88 
+
89 
+   set(fig, 'menubar', 'none');
90 
+
91 
+   if isempty(nii_menu.Mfile)
92 
+      nii_menu.Mfile = uimenu('Parent',fig, ...
93 
+   	   'Label','File');
94 
+
95 
+      nii_menu.Mfile_save = uimenu('Parent',nii_menu.Mfile, ...
96 
+   	   'Label','Save displayed image as ...', ...
97 
+           'Callback','view_nii_menu(''save_disp'');');
98 
+   else
99 
+      nii_menu.Mfile_save = uimenu('Parent',nii_menu.Mfile, ...
100 
+   	   'Label','Save displayed image as ...', ...
101 
+           'separator','on', ...
102 
+           'Callback','view_nii_menu(''save_disp'');');
103 
+   end
104 
+
105 
+   if isempty(nii_menu.Medit)
106 
+      nii_menu.Medit = uimenu('Parent',fig, ...
107 
+   	   'Label','Edit');
108 
+
109 
+      nii_menu.Medit_orient = uimenu('Parent',nii_menu.Medit, ...
110 
+   	   'Label','Convert to RAS orientation', ...
111 
+           'Callback','view_nii_menu(''orient'');');
112 
+   else
113 
+      nii_menu.Medit_orient = uimenu('Parent',nii_menu.Medit, ...
114 
+   	   'Label','Convert to RAS orientation', ...
115 
+           'separator','on', ...
116 
+           'Callback','view_nii_menu(''orient'');');
117 
+   end
118 
+
119 
+   if isempty(nii_menu.Mview)
120 
+      nii_menu.Mview = uimenu('Parent',fig, ...
121 
+   	   'Label','View');
122 
+
123 
+      nii_menu.Mview_info = uimenu('Parent',nii_menu.Mview, ...
124 
+   	   'Label','Image Information', ...
125 
+           'Callback','view_nii_menu(''img_info'');');
126 
+   else
127 
+      nii_menu.Mview_info = uimenu('Parent',nii_menu.Mview, ...
128 
+   	   'Label','Image Information', ...
129 
+           'separator','on', ...
130 
+           'Callback','view_nii_menu(''img_info'');');
131 
+   end
132 
+
133 
+   nii_menu.Mzoom = rri_zoom_menu(fig);
134 
+
135 
+   nii_menu.Minterp = uimenu('Parent',fig, ...
136 
+   	   'Label','Interp on', ...
137 
+	   'Userdata', 1, ...
138 
+           'Callback','view_nii_menu(''interp'');');
139 
+
140 
+   setappdata(fig,'nii_menu',nii_menu);
141 
+   menu_hdl = nii_menu.Minterp;
142 
+
143 
+   return					% init
144 
+
145 
+
146 
+%----------------------------------------------------------------
147 
+function reset_zoom(fig)
148 
+
149 
+   old_handle_vis = get(fig, 'HandleVisibility');
150 
+   set(fig, 'HandleVisibility', 'on');
151 
+
152 
+   nii_view = getappdata(fig, 'nii_view');
153 
+   nii_menu = getappdata(fig, 'nii_menu');
154 
+
155 
+   set(nii_menu.Mzoom,'Userdata',1,'Label','Zoom on');
156 
+   set(fig,'pointer','arrow');
157 
+   zoom off;
158 
+
159 
+   axes(nii_view.handles.axial_axes);
160 
+   setappdata(get(gca,'zlabel'), 'ZOOMAxesData', ...
161 
+			[get(gca, 'xlim') get(gca, 'ylim')])
162 
+%   zoom reset;
163 
+ %  zoom getlimits;
164 
+   zoom out;
165 
+
166 
+   axes(nii_view.handles.coronal_axes);
167 
+   setappdata(get(gca,'zlabel'), 'ZOOMAxesData', ...
168 
+			[get(gca, 'xlim') get(gca, 'ylim')])
169 
+%   zoom reset;
170 
+ %  zoom getlimits;
171 
+   zoom out;
172 
+
173 
+   axes(nii_view.handles.sagittal_axes);
174 
+   setappdata(get(gca,'zlabel'), 'ZOOMAxesData', ...
175 
+			[get(gca, 'xlim') get(gca, 'ylim')])
176 
+%   zoom reset;
177 
+ %  zoom getlimits;
178 
+   zoom out;
179 
+
180 
+   set(fig, 'HandleVisibility', old_handle_vis);
181 
+
182 
+   return;					% reset_zoom
183 
+
184 
+
185 
+%----------------------------------------------------------------
186 
+function img_info
187 
+
188 
+   nii_view = getappdata(gcbf, 'nii_view');
189 
+   hdr = nii_view.nii.hdr;
190 
+
191 
+   max_value = num2str(double(max(nii_view.nii.img(:))));
192 
+   min_value = num2str(double(min(nii_view.nii.img(:))));
193 
+
194 
+   dim = sprintf('%d  %d  %d', double(hdr.dime.dim(2:4)));
195 
+   vox = sprintf('%.3f  %.3f  %.3f', double(hdr.dime.pixdim(2:4)));
196 
+
197 
+   if double(hdr.dime.datatype) == 1
198 
+      type = '1-bit binary';
199 
+   elseif double(hdr.dime.datatype) == 2
200 
+      type = '8-bit unsigned integer';
201 
+   elseif double(hdr.dime.datatype) == 4
202 
+      type = '16-bit signed integer';
203 
+   elseif double(hdr.dime.datatype) == 8
204 
+      type = '32-bit signed integer';
205 
+   elseif double(hdr.dime.datatype) == 16
206 
+      type = '32-bit single float';
207 
+   elseif double(hdr.dime.datatype) == 64
208 
+      type = '64-bit double precision';
209 
+   elseif double(hdr.dime.datatype) == 128
210 
+      type = '24-bit RGB true color';
211 
+   elseif double(hdr.dime.datatype) == 256
212 
+      type = '8-bit signed integer';
213 
+   elseif double(hdr.dime.datatype) == 511
214 
+      type = '96-bit RGB true color';
215 
+   elseif double(hdr.dime.datatype) == 512
216 
+      type = '16-bit unsigned integer';
217 
+   elseif double(hdr.dime.datatype) == 768
218 
+      type = '32-bit unsigned integer';
219 
+   elseif double(hdr.dime.datatype) == 1024
220 
+      type = '64-bit signed integer';
221 
+   elseif double(hdr.dime.datatype) == 1280
222 
+      type = '64-bit unsigned integer';
223 
+   end
224 
+
225 
+   msg = {};
226 
+   msg = [msg {''}];
227 
+   msg = [msg {['Dimension:  [', dim, ']']}];
228 
+   msg = [msg {''}];
229 
+   msg = [msg {['Voxel Size:  [', vox, ']']}];
230 
+   msg = [msg {''}];
231 
+   msg = [msg {['Data Type:  [', type, ']']}];
232 
+   msg = [msg {''}];
233 
+   msg = [msg {['Max Value:  [', max_value, ']']}];
234 
+   msg = [msg {''}];
235 
+   msg = [msg {['Min Value:  [', min_value, ']']}];
236 
+   msg = [msg {''}];
237 
+
238 
+   if isfield(nii_view.nii, 'fileprefix')
239 
+      if isfield(nii_view.nii, 'filetype') & nii_view.nii.filetype == 2
240 
+         msg = [msg {['File Name:  [', nii_view.nii.fileprefix, '.nii]']}];
241 
+         msg = [msg {''}];
242 
+      elseif isfield(nii_view.nii, 'filetype')
243 
+         msg = [msg {['File Name:  [', nii_view.nii.fileprefix, '.img]']}];
244 
+         msg = [msg {''}];
245 
+      else
246 
+         msg = [msg {['File Prefix:  [', nii_view.nii.fileprefix, ']']}];
247 
+         msg = [msg {''}];
248 
+      end
249 
+   end
250 
+
251 
+   h = msgbox(msg, 'Image Information', 'modal');
252 
+   set(h,'color',[1 1 1]);
253 
+
254 
+   return;					% img_info
255 
+
256 
+
257 
+%----------------------------------------------------------------
258 
+function orient
259 
+
260 
+   fig = gcbf;
261 
+   nii_view = getappdata(fig, 'nii_view');
262 
+   nii = nii_view.nii;
263 
+
264 
+   old_pointer = get(fig,'Pointer');
265 
+   set(fig,'Pointer','watch');
266 
+
267 
+   [nii orient] = rri_orient(nii);
268 
+
269 
+   if isequal(orient, [1 2 3])		% do nothing
270 
+      set(fig,'Pointer',old_pointer);
271 
+      return;
272 
+   end
273 
+
274 
+   oldopt = view_nii(fig);
275 
+   opt.setarea = oldopt.area;
276 
+   opt.usecolorbar = oldopt.usecolorbar;
277 
+   opt.usecrosshair = oldopt.usecrosshair;
278 
+   opt.usestretch = oldopt.usestretch;
279 
+   opt.useimagesc = oldopt.useimagesc;
280 
+   opt.useinterp = oldopt.useinterp;
281 
+   opt.command = 'updatenii';
282 
+
283 
+   view_nii(fig, nii, opt);
284 
+   set(fig,'Pointer',old_pointer);
285 
+   reset_zoom(fig);
286 
+
287 
+   return;					% orient
288 
+
289 
+
290 
+%----------------------------------------------------------------
291 
+function save_disp
292 
+
293 
+   [filename pathname] = uiputfile('*.*', 'Save displayed image as (*.nii or *.img)');
294 
+
295 
+   if isequal(filename,0) | isequal(pathname,0)
296 
+      return;
297 
+   else
298 
+      out_imgfile = fullfile(pathname, filename);	% original image file
299 
+   end
300 
+
301 
+   old_pointer = get(gcbf,'Pointer');
302 
+   set(gcbf,'Pointer','watch');
303 
+
304 
+   nii_view = getappdata(gcbf, 'nii_view');
305 
+   nii = nii_view.nii;
306 
+
307 
+   try
308 
+      save_nii(nii, out_imgfile);
309 
+   catch
310 
+      msg = 'File can not be saved.';
311 
+      msgbox(msg, 'File write error', 'modal');
312 
+   end
313 
+
314 
+   set(gcbf,'Pointer',old_pointer);
315 
+
316 
+   return;					% save_disp
317 
+
NIFTI_20090325/xform_nii.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,488 @@
1 
+%  internal function
2 
+
3 
+%  'xform_nii.m' is an internal function called by "load_nii.m", so
4 
+%  you do not need run this program by yourself. It does simplified
5 
+%  NIfTI sform/qform affine transform, and supports some of the
6 
+%  affine transforms, including translation, reflection, and
7 
+%  orthogonal rotation (N*90 degree).
8 
+%
9 
+%  For other affine transforms, e.g. any degree rotation, shearing
10 
+%  etc. you will have to use the included 'reslice_nii.m' program
11 
+%  to reslice the image volume. 'reslice_nii.m' is not called by
12 
+%  any other program, and you have to run 'reslice_nii.m' explicitly
13 
+%  for those NIfTI files that you want to reslice them.
14 
+%
15 
+%  Since 'xform_nii.m' does not involve any interpolation or any
16 
+%  slice change, the original image volume is supposed to be
17 
+%  untouched, although it is translated, reflected, or even
18 
+%  orthogonally rotated, based on the affine matrix in the
19 
+%  NIfTI header.
20 
+%
21 
+%  However, the affine matrix in the header of a lot NIfTI files
22 
+%  contain slightly non-orthogonal rotation. Therefore, optional
23 
+%  input parameter 'tolerance' is used to allow some distortion
24 
+%  in the loaded image for any non-orthogonal rotation or shearing
25 
+%  of NIfTI affine matrix. If you set 'tolerance' to 0, it means
26 
+%  that you do not allow any distortion. If you set 'tolerance' to
27 
+%  1, it means that you do not care any distortion. The image will
28 
+%  fail to be loaded if it can not be tolerated. The tolerance will
29 
+%  be set to 0.1 (10%), if it is default or empty.
30 
+%
31 
+%  Because 'reslice_nii.m' has to perform 3D interpolation, it can
32 
+%  be slow depending on image size and affine matrix in the header.
33 
+%
34 
+%  After you perform the affine transform, the 'nii' structure
35 
+%  generated from 'xform_nii.m' or new NIfTI file created from
36 
+%  'reslice_nii.m' will be in RAS orientation, i.e. X axis from
37 
+%  Left to Right, Y axis from Posterior to Anterior, and Z axis
38 
+%  from Inferior to Superior.
39 
+%
40 
+%  NOTE: This function should be called immediately after load_nii.
41 
+%
42 
+%  Usage: [ nii ] = xform_nii(nii, [tolerance], [preferredForm])
43 
+%
44 
+%  nii	- NIFTI structure (returned from load_nii)
45 
+%
46 
+%  tolerance (optional) - distortion allowed for non-orthogonal rotation
47 
+%	or shearing in NIfTI affine matrix. It will be set to 0.1 (10%),
48 
+%	if it is default or empty.
49 
+%
50 
+%  preferredForm (optional)  -  selects which transformation from voxels
51 
+%	to RAS coordinates; values are s,q,S,Q.  Lower case s,q indicate
52 
+%	"prefer sform or qform, but use others if preferred not present".
53 
+%	Upper case indicate the program is forced to use the specificied
54 
+%	tranform or fail loading.  'preferredForm' will be 's', if it is
55 
+%	default or empty.	- Jeff Gunter
56 
+%
57 
+%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
58 
+%
59 
+%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
60 
+%
61 
+function nii = xform_nii(nii, tolerance, preferredForm)
62 
+
63 
+   %  save a copy of the header as it was loaded.  This is the
64 
+   %  header before any sform, qform manipulation is done.
65 
+   %
66 
+   nii.original.hdr = nii.hdr;
67 
+
68 
+   if ~exist('tolerance','var') | isempty(tolerance)
69 
+      tolerance = 0.1;
70 
+   elseif(tolerance<=0)
71 
+      tolerance = eps;
72 
+   end
73 
+
74 
+   if ~exist('preferredForm','var') | isempty(preferredForm)
75 
+      preferredForm= 's';				% Jeff
76 
+   end
77 
+
78 
+   %  if scl_slope field is nonzero, then each voxel value in the
79 
+   %  dataset should be scaled as: y = scl_slope * x + scl_inter
80 
+   %  I bring it here because hdr will be modified by change_hdr.
81 
+   %
82 
+   if nii.hdr.dime.scl_slope ~= 0 & ...
83 
+	ismember(nii.hdr.dime.datatype, [2,4,8,16,64,256,512,768]) & ...
84 
+	(nii.hdr.dime.scl_slope ~= 1 | nii.hdr.dime.scl_inter ~= 0)
85 
+
86 
+      nii.img = ...
87 
+	nii.hdr.dime.scl_slope * double(nii.img) + nii.hdr.dime.scl_inter;
88 
+
89 
+      if nii.hdr.dime.datatype == 64
90 
+
91 
+         nii.hdr.dime.datatype = 64;
92 
+         nii.hdr.dime.bitpix = 64;
93 
+      else
94 
+         nii.img = single(nii.img);
95 
+
96 
+         nii.hdr.dime.datatype = 16;
97 
+         nii.hdr.dime.bitpix = 32;
98 
+      end
99 
+
100 
+      nii.hdr.dime.glmax = max(double(nii.img(:)));
101 
+      nii.hdr.dime.glmin = min(double(nii.img(:)));
102 
+
103 
+      %  set scale to non-use, because it is applied in xform_nii
104 
+      %
105 
+      nii.hdr.dime.scl_slope = 0;
106 
+
107 
+   end
108 
+
109 
+   %  However, the scaling is to be ignored if datatype is DT_RGB24.
110 
+
111 
+   %  If datatype is a complex type, then the scaling is to be applied
112 
+   %  to both the real and imaginary parts.
113 
+   %
114 
+   if nii.hdr.dime.scl_slope ~= 0 & ...
115 
+	ismember(nii.hdr.dime.datatype, [32,1792])
116 
+
117 
+      nii.img = ...
118 
+	nii.hdr.dime.scl_slope * double(nii.img) + nii.hdr.dime.scl_inter;
119 
+
120 
+      if nii.hdr.dime.datatype == 32
121 
+         nii.img = single(nii.img);
122 
+      end
123 
+
124 
+      nii.hdr.dime.glmax = max(double(nii.img(:)));
125 
+      nii.hdr.dime.glmin = min(double(nii.img(:)));
126 
+
127 
+      %  set scale to non-use, because it is applied in xform_nii
128 
+      %
129 
+      nii.hdr.dime.scl_slope = 0;
130 
+
131 
+   end
132 
+
133 
+   %  There is no need for this program to transform Analyze data
134 
+   %
135 
+   if nii.filetype == 0 & exist([nii.fileprefix '.mat'],'file')
136 
+      load([nii.fileprefix '.mat']);	% old SPM affine matrix
137 
+      R=M(1:3,1:3);
138 
+      T=M(1:3,4);
139 
+      T=R*ones(3,1)+T;
140 
+      M(1:3,4)=T;
141 
+      nii.hdr.hist.qform_code=0;
142 
+      nii.hdr.hist.sform_code=1;
143 
+      nii.hdr.hist.srow_x=M(1,:);
144 
+      nii.hdr.hist.srow_y=M(2,:);
145 
+      nii.hdr.hist.srow_z=M(3,:);
146 
+   elseif nii.filetype == 0
147 
+      nii.hdr.hist.rot_orient = [];
148 
+      nii.hdr.hist.flip_orient = [];
149 
+      return;				% no sform/qform for Analyze format
150 
+   end
151 
+
152 
+   hdr = nii.hdr;
153 
+
154 
+   [hdr,orient]=change_hdr(hdr,tolerance,preferredForm);
155 
+
156 
+   %  flip and/or rotate image data
157 
+   %
158 
+   if ~isequal(orient, [1 2 3])
159 
+
160 
+      old_dim = hdr.dime.dim([2:4]);
161 
+
162 
+      %  More than 1 time frame
163 
+      %
164 
+      if ndims(nii.img) > 3
165 
+         pattern = 1:prod(old_dim);
166 
+      else
167 
+         pattern = [];
168 
+      end
169 
+
170 
+      if ~isempty(pattern)
171 
+         pattern = reshape(pattern, old_dim);
172 
+      end
173 
+
174 
+      %  calculate for rotation after flip
175 
+      %
176 
+      rot_orient = mod(orient + 2, 3) + 1;
177 
+
178 
+      %  do flip:
179 
+      %
180 
+      flip_orient = orient - rot_orient;
181 
+
182 
+      for i = 1:3
183 
+         if flip_orient(i)
184 
+            if ~isempty(pattern)
185 
+               pattern = flipdim(pattern, i);
186 
+            else
187 
+               nii.img = flipdim(nii.img, i);
188 
+            end
189 
+         end
190 
+      end
191 
+
192 
+      %  get index of orient (rotate inversely)
193 
+      %
194 
+      [tmp rot_orient] = sort(rot_orient);
195 
+
196 
+      new_dim = old_dim;
197 
+      new_dim = new_dim(rot_orient);
198 
+      hdr.dime.dim([2:4]) = new_dim;
199 
+
200 
+      new_pixdim = hdr.dime.pixdim([2:4]);
201 
+      new_pixdim = new_pixdim(rot_orient);
202 
+      hdr.dime.pixdim([2:4]) = new_pixdim;
203 
+
204 
+      %  re-calculate originator
205 
+      %
206 
+      tmp = hdr.hist.originator([1:3]);
207 
+      tmp = tmp(rot_orient);
208 
+      flip_orient = flip_orient(rot_orient);
209 
+
210 
+      for i = 1:3
211 
+         if flip_orient(i) & ~isequal(tmp(i), 0)
212 
+            tmp(i) = new_dim(i) - tmp(i) + 1;
213 
+         end
214 
+      end
215 
+
216 
+      hdr.hist.originator([1:3]) = tmp;
217 
+      hdr.hist.rot_orient = rot_orient;
218 
+      hdr.hist.flip_orient = flip_orient;
219 
+
220 
+      %  do rotation:
221 
+      %
222 
+      if ~isempty(pattern)
223 
+         pattern = permute(pattern, rot_orient);
224 
+         pattern = pattern(:);
225 
+
226 
+         nii.img = reshape(nii.img, [prod(new_dim) hdr.dime.dim(5:8)]);
227 
+         nii.img = nii.img(pattern, :);
228 
+         nii.img = reshape(nii.img, [new_dim       hdr.dime.dim(5:8)]);
229 
+      else
230 
+         nii.img = permute(nii.img, rot_orient);
231 
+      end
232 
+   else
233 
+      hdr.hist.rot_orient = [];
234 
+      hdr.hist.flip_orient = [];
235 
+   end
236 
+
237 
+   nii.hdr = hdr;
238 
+
239 
+   return;					% xform_nii
240 
+
241 
+
242 
+%-----------------------------------------------------------------------
243 
+function [hdr, orient] = change_hdr(hdr, tolerance, preferredForm)
244 
+
245 
+   orient = [1 2 3];
246 
+   affine_transform = 1;
247 
+
248 
+   %  NIFTI can have both sform and qform transform. This program
249 
+   %  will check sform_code prior to qform_code by default.
250 
+   %
251 
+   %  If user specifys "preferredForm", user can then choose the
252 
+   %  priority.					- Jeff
253 
+   %
254 
+   useForm=[];					% Jeff
255 
+
256 
+   if isequal(preferredForm,'S')
257 
+       if isequal(hdr.hist.sform_code,0)
258 
+           error('User requires sform, sform not set in header');
259 
+       else
260 
+           useForm='s';
261 
+       end
262 
+   end						% Jeff
263 
+
264 
+   if isequal(preferredForm,'Q')
265 
+       if isequal(hdr.hist.qform_code,0)
266 
+           error('User requires qform, qform not set in header');
267 
+       else
268 
+           useForm='q';
269 
+       end
270 
+   end						% Jeff
271 
+
272 
+   if isequal(preferredForm,'s')
273 
+       if hdr.hist.sform_code > 0
274 
+           useForm='s';
275 
+       elseif hdr.hist.qform_code > 0
276 
+           useForm='q';
277 
+       end
278 
+   end						% Jeff
279 
+
280 
+   if isequal(preferredForm,'q')
281 
+       if hdr.hist.qform_code > 0
282 
+           useForm='q';
283 
+       elseif hdr.hist.sform_code > 0
284 
+           useForm='s';
285 
+       end
286 
+   end						% Jeff
287 
+
288 
+   if isequal(useForm,'s')
289 
+      R = [hdr.hist.srow_x(1:3)
290 
+           hdr.hist.srow_y(1:3)
291 
+           hdr.hist.srow_z(1:3)];
292 
+
293 
+      T = [hdr.hist.srow_x(4)
294 
+           hdr.hist.srow_y(4)
295 
+           hdr.hist.srow_z(4)];
296 
+
297 
+      if det(R) == 0 | ~isequal(R(find(R)), sum(R)')
298 
+         hdr.hist.old_affine = [ [R;[0 0 0]] [T;1] ];
299 
+         R_sort = sort(abs(R(:)));
300 
+         R( find( abs(R) < tolerance*min(R_sort(end-2:end)) ) ) = 0;
301 
+         hdr.hist.new_affine = [ [R;[0 0 0]] [T;1] ];
302 
+
303 
+         if det(R) == 0 | ~isequal(R(find(R)), sum(R)')
304 
+            msg = [char(10) char(10) '   Non-orthogonal rotation or shearing '];
305 
+            msg = [msg 'found inside the affine matrix' char(10)];
306 
+            msg = [msg '   in this NIfTI file. You have 3 options:' char(10) char(10)];
307 
+            msg = [msg '   1. Using included ''reslice_nii.m'' program to reslice the NIfTI' char(10)];
308 
+            msg = [msg '      file. I strongly recommand this, because it will not cause' char(10)];
309 
+            msg = [msg '      negative effect, as long as you remember not to do slice' char(10)];
310 
+            msg = [msg '      time correction after using ''reslice_nii.m''.' char(10) char(10)];
311 
+            msg = [msg '   2. Using included ''load_untouch_nii.m'' program to load image' char(10)];
312 
+            msg = [msg '      without applying any affine geometric transformation or' char(10)];
313 
+            msg = [msg '      voxel intensity scaling. This is only for people who want' char(10)];
314 
+            msg = [msg '      to do some image processing regardless of image orientation' char(10)];
315 
+            msg = [msg '      and to save data back with the same NIfTI header.' char(10) char(10)];
316 
+            msg = [msg '   3. Increasing the tolerance to allow more distortion in loaded' char(10)];
317 
+            msg = [msg '      image, but I don''t suggest this.' char(10) char(10)];
318 
+            msg = [msg '   To get help, please type:' char(10) char(10) '   help reslice_nii.m' char(10)];
319 
+            msg = [msg '   help load_untouch_nii.m' char(10) '   help load_nii.m'];
320 
+            error(msg);
321 
+         end
322 
+      end
323 
+
324 
+   elseif isequal(useForm,'q')
325 
+      b = hdr.hist.quatern_b;
326 
+      c = hdr.hist.quatern_c;
327 
+      d = hdr.hist.quatern_d;
328 
+
329 
+      if 1.0-(b*b+c*c+d*d) < 0
330 
+         if abs(1.0-(b*b+c*c+d*d)) < 1e-5
331 
+            a = 0;
332 
+         else
333 
+            error('Incorrect quaternion values in this NIFTI data.');
334 
+         end
335 
+      else
336 
+         a = sqrt(1.0-(b*b+c*c+d*d));
337 
+      end
338 
+
339 
+      qfac = hdr.dime.pixdim(1);
340 
+      i = hdr.dime.pixdim(2);
341 
+      j = hdr.dime.pixdim(3);
342 
+      k = qfac * hdr.dime.pixdim(4);
343 
+
344 
+      R = [a*a+b*b-c*c-d*d     2*b*c-2*a*d        2*b*d+2*a*c
345 
+           2*b*c+2*a*d         a*a+c*c-b*b-d*d    2*c*d-2*a*b
346 
+           2*b*d-2*a*c         2*c*d+2*a*b        a*a+d*d-c*c-b*b];
347 
+
348 
+      T = [hdr.hist.qoffset_x
349 
+           hdr.hist.qoffset_y
350 
+           hdr.hist.qoffset_z];
351 
+
352 
+      %  qforms are expected to generate rotation matrices R which are
353 
+      %  det(R) = 1; we'll make sure that happens.
354 
+      %
355 
+      %  now we make the same checks as were done above for sform data
356 
+      %  BUT we do it on a transform that is in terms of voxels not mm;
357 
+      %  after we figure out the angles and squash them to closest
358 
+      %  rectilinear direction. After that, the voxel sizes are then
359 
+      %  added.
360 
+      %
361 
+      %  This part is modified by Jeff Gunter.
362 
+      %
363 
+      if det(R) == 0 | ~isequal(R(find(R)), sum(R)')
364 
+
365 
+         %  det(R) == 0 is not a common trigger for this ---
366 
+         %  R(find(R)) is a list of non-zero elements in R; if that
367 
+         %  is straight (not oblique) then it should be the same as
368 
+         %  columnwise summation. Could just as well have checked the
369 
+         %  lengths of R(find(R)) and sum(R)' (which should be 3)
370 
+         %
371 
+         hdr.hist.old_affine = [ [R * diag([i j k]);[0 0 0]] [T;1] ];
372 
+         R_sort = sort(abs(R(:)));
373 
+         R( find( abs(R) < tolerance*min(R_sort(end-2:end)) ) ) = 0;
374 
+         R = R * diag([i j k]);
375 
+         hdr.hist.new_affine = [ [R;[0 0 0]] [T;1] ];
376 
+
377 
+         if det(R) == 0 | ~isequal(R(find(R)), sum(R)')
378 
+            msg = [char(10) char(10) '   Non-orthogonal rotation or shearing '];
379 
+            msg = [msg 'found inside the affine matrix' char(10)];
380 
+            msg = [msg '   in this NIfTI file. You have 3 options:' char(10) char(10)];
381 
+            msg = [msg '   1. Using included ''reslice_nii.m'' program to reslice the NIfTI' char(10)];
382 
+            msg = [msg '      file. I strongly recommand this, because it will not cause' char(10)];
383 
+            msg = [msg '      negative effect, as long as you remember not to do slice' char(10)];
384 
+            msg = [msg '      time correction after using ''reslice_nii.m''.' char(10) char(10)];
385 
+            msg = [msg '   2. Using included ''load_untouch_nii.m'' program to load image' char(10)];
386 
+            msg = [msg '      without applying any affine geometric transformation or' char(10)];
387 
+            msg = [msg '      voxel intensity scaling. This is only for people who want' char(10)];
388 
+            msg = [msg '      to do some image processing regardless of image orientation' char(10)];
389 
+            msg = [msg '      and to save data back with the same NIfTI header.' char(10) char(10)];
390 
+            msg = [msg '   3. Increasing the tolerance to allow more distortion in loaded' char(10)];
391 
+            msg = [msg '      image, but I don''t suggest this.' char(10) char(10)];
392 
+            msg = [msg '   To get help, please type:' char(10) char(10) '   help reslice_nii.m' char(10)];
393 
+            msg = [msg '   help load_untouch_nii.m' char(10) '   help load_nii.m'];
394 
+            error(msg);
395 
+         end
396 
+
397 
+      else
398 
+         R = R * diag([i j k]);
399 
+      end					% 1st det(R)
400 
+
401 
+   else
402 
+      affine_transform = 0;	% no sform or qform transform
403 
+   end
404 
+
405 
+   if affine_transform == 1
406 
+      voxel_size = abs(sum(R,1));
407 
+      inv_R = inv(R);
408 
+      originator = inv_R*(-T)+1;
409 
+      orient = get_orient(inv_R);
410 
+
411 
+      %  modify pixdim and originator
412 
+      %
413 
+      hdr.dime.pixdim(2:4) = voxel_size;
414 
+      hdr.hist.originator(1:3) = originator;
415 
+
416 
+      %  set sform or qform to non-use, because they have been
417 
+      %  applied in xform_nii
418 
+      %
419 
+      hdr.hist.qform_code = 0;
420 
+      hdr.hist.sform_code = 0;
421 
+   end
422 
+
423 
+   %  apply space_unit to pixdim if not 1 (mm)
424 
+   %
425 
+   space_unit = get_units(hdr);
426 
+
427 
+   if space_unit ~= 1
428 
+      hdr.dime.pixdim(2:4) = hdr.dime.pixdim(2:4) * space_unit;
429 
+
430 
+      %  set space_unit of xyzt_units to millimeter, because
431 
+      %  voxel_size has been re-scaled
432 
+      %
433 
+      hdr.dime.xyzt_units = char(bitset(hdr.dime.xyzt_units,1,0));
434 
+      hdr.dime.xyzt_units = char(bitset(hdr.dime.xyzt_units,2,1));
435 
+      hdr.dime.xyzt_units = char(bitset(hdr.dime.xyzt_units,3,0));
436 
+   end
437 
+
438 
+   return;					% change_hdr
439 
+
440 
+
441 
+%-----------------------------------------------------------------------
442 
+function orient = get_orient(R)
443 
+
444 
+   orient = [];
445 
+
446 
+   for i = 1:3
447 
+      switch find(R(i,:)) * sign(sum(R(i,:)))
448 
+      case 1
449 
+         orient = [orient 1];		% Left to Right
450 
+      case 2
451 
+         orient = [orient 2];		% Posterior to Anterior
452 
+      case 3
453 
+         orient = [orient 3];		% Inferior to Superior
454 
+      case -1
455 
+         orient = [orient 4];		% Right to Left
456 
+      case -2
457 
+         orient = [orient 5];		% Anterior to Posterior
458 
+      case -3
459 
+         orient = [orient 6];		% Superior to Inferior
460 
+      end
461 
+   end
462 
+
463 
+   return;					% get_orient
464 
+
465 
+
466 
+%-----------------------------------------------------------------------
467 
+function [space_unit, time_unit] = get_units(hdr)
468 
+
469 
+   switch bitand(hdr.dime.xyzt_units, 7)	% mask with 0x07
470 
+   case 1
471 
+      space_unit = 1e+3;		% meter, m
472 
+   case 3
473 
+      space_unit = 1e-3;		% micrometer, um
474 
+   otherwise
475 
+      space_unit = 1;			% millimeter, mm
476 
+   end
477 
+
478 
+   switch bitand(hdr.dime.xyzt_units, 56)	% mask with 0x38
479 
+   case 16
480 
+      time_unit = 1e-3;			% millisecond, ms
481 
+   case 24
482 
+      time_unit = 1e-6;			% microsecond, us
483 
+   otherwise
484 
+      time_unit = 1;			% second, s
485 
+   end
486 
+
487 
+   return;					% get_units
488 
+
private/fbs_buildSphere.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,28 @@
1 
+function sphere = fbs_buildSphere(mapping,center,radius,vdim)
2 
+iVoxel = 1;
3 
+% returns the IDs within Sphere
4 
+coord = mapping.indexToCoordMap.get(center);
5 
+
6 
+vxrad = ceil((radius*ones(1,3))./(ones(1,1)*vdim))';
7 
+
8 
+[x y z] = ndgrid(-vxrad(1,iVoxel):sign(vdim(1)):vxrad(1,iVoxel), ...
9 
+    -vxrad(2,iVoxel):sign(vdim(2)):vxrad(2,iVoxel), ...
10 
+    -vxrad(3,iVoxel):sign(vdim(3)):vxrad(3,iVoxel));
11 
+sel = (x./vxrad(1,iVoxel)).^2 + (y./vxrad(2,iVoxel)).^2 + ...
12 
+    (z./vxrad(3,iVoxel)).^2 <= 1;
13 
+
14 
+x = coord(1,1)+x(sel(:));
15 
+y = coord(2,1)+y(sel(:));
16 
+z = coord(3,1)+z(sel(:));
17 
+
18 
+sphere = [];
19 
+for iCoord = 1:size(x,1);
20 
+       key = java.util.Vector(3,0);
21 
+        key.add(0,x(iCoord));
22 
+        key.add(1,y(iCoord));
23 
+        key.add(2,z(iCoord));
24 
+    id = mapping.coordToIndexMap.get(key);
25 
+    sphere = [sphere id];
26 
+end
27 
+
28 
+end
0 29 
\ No newline at end of file
private/fbs_coordtable_getCoord.m
Zeige Datei @ 87b08fd
... ... 
@@ -0,0 +1,7 @@
1 
+function id = fbs_coordtable_getIndex(table,coord)
2 
+if table.containsKey(coord)
3 
+    id = table.get(coord);
4 
+else
5 
+     error('FBS:getLabel:noSuchValue','this Mapping does not contain a Value %d',condition);
6 
+end
7 
+end
0 8 
\ No newline at end of file
private/main.m
Zeige Datei @ 87b08fd
... ... 
@@ -141,6 +141,8 @@ switch task
141 141 
         disp('not implemented')
142 142 
     case 'FBS'
143 143 
         disp('this method is under high development.')
144 
+        fbsargs.svmopts = getSvmArgs(model,1);
145 
+        header.svmrnd   = getSvmRnd(model);
144 146 
         fbsargs.radius  = getSearchlightRadius(model);
145 147 
             runFBSImageMaskMode(header,data,fbsargs);
146 148
private/runFBSImageMaskMode.m
Zeige Datei @ 87b08fd
... ... 
@@ -1,4 +1,6 @@
1 1 
 function output =  runFBSImageMaskMode(header,subjectdata,fbsargs)
2 
+addpath('NIFTI_20090325');
3 
+
2 4 
 args = header.args;
3 5
4 6 
 subjects = subjectdata;
... ... 
@@ -21,36 +23,47 @@ timePointArgs.eventList     = header.classDef.eventMatrix;
21 23 
 timeLineStart  = timeline.frameShiftStart;
22 24 
 timeLineEnd    = timeline.frameShiftEnd;
23 25
26 
+RANDOMIZE_DATAPOINTS = header.svmrnd;
27 
+svmopts = fbsargs.svmopts;
28 
+
24 29 
 disp(sprintf('batch processing  %g subjects.',nSubjects));
25 30
26 31 
 for s = 1:nSubjects
27 
-
32 
+    elapsed = struct; %measure the timing
28 33 
     disp(sprintf('processing subject %s.',subjects{s}.name));
29 34 
     % load image data
30 35
31 36 
     disp('fetching volume definitions, please wait');
37 
+    tic;
32 38 
     volumes = spm_vol(getImageFileList(subjects{s}.dir,sessionlist,args.mask));
33 
-
39 
+    elapsed.loadList = toc;
34 40 
     disp('computing volume values, please wait');
35 
-
41 
+    tic
36 42 
     [extr x y z] = calculateRoiImageData(volumes,subjects{s}.roiFile);
43 
+    elapsed.calcExtr = toc;
37 44
38 45 
 clear volumes; %save memory ??
39 46 
 disp('cleared volumes');
40 
-
47 
+tic
41 48
42 49 
     nVoxel = size(extr(1).dat,1);
43 50
44 51 
     indexToCoordMap = java.util.HashMap;
45 52 
     coordToIndexMap = java.util.HashMap;
46 53 
     for iVoxel = 1:nVoxel
47 
-        coord = [x(iVoxel),y(iVoxel),z(iVoxel)];
54 
+        coord = [x(iVoxel) y(iVoxel) z(iVoxel)];
55 
+        a = java.util.Vector(3,0);
56 
+        a.add(0,coord(1));
57 
+        a.add(1,coord(2));
58 
+        a.add(2,coord(3));
48 59 
         indexToCoordMap.put(iVoxel,coord);
49 
-        coordToIndexMap.put(coord,iVoxel);
60 
+        coordToIndexMap.put(a,iVoxel);
50 61 
     end
51 62
52 
-    subjects{s}.indexToCoordMap = indexToCoordMap;
53 
-    subjects{s}.coordToIndexMap = coordToIndexMap;
63 
+    mapping.indexToCoordMap = indexToCoordMap;
64 
+    mapping.coordToIndexMap = coordToIndexMap;
65 
+
66 
+    elapsed.mapping = toc;
54 67
55 68 
     % calculate psth
56 69
... ... 
@@ -58,6 +71,7 @@ disp('cleared volumes');
58 71 
     pstopts.des = subjects{s}.des;
59 72
60 73 
     disp(sprintf('computing psth for %g voxel.',nVoxel));
74 
+tic
61 75
62 76 
     for iVoxel = 1:nVoxel
63 77 
         rawdata = [];
... ... 
@@ -73,49 +87,74 @@ disp('cleared volumes');
73 87 
              sprintf(' %g%%\t complete',p);
74 88 
          end
75 89 
     end
90 
+elapsed.psth = toc;
76 91 
     disp('psth done');
77 92 
     warning(warn);
93 
+    clear extr;
78 94 
     %run searchlight
79 
-
80 
-
95 
+tic
81 96
82 97 
     display(sprintf('rastering %g coordinates with approx. %g mm radius',nVoxel,radius));
83 98 
     % for each timeslice
84 
-
85 
-    for index = 1:timeLineEnd-timeLineStart+1
86 
-        timeShift = index;
99 
+    globalStart = timeline.psthStart;
100 
+    globalEnd = timeline.psthEnd;
101 
+    decodeDuration = timeline.decodeDuration;
102 
+    labelMap = timePointArgs.labelMap;
103 
+    eventList = pstopts.eventList;
104 
+
105 
+    img3D = [];
106 
+    % tmp = spm_imatrix(V(kImage).mat); %
107 
+    % vdim = tmp(7:9); % Voxel-Size
108 
+    vdim = [3,3,3.5];
109 
+
110 
+    for timeShift = 1:timeLineEnd-timeLineStart+1
87 111 
     % center timepoint && relative shift
88 112 
     frameStart  = floor(-globalStart+1+timeShift - 0.5*decodeDuration);
89 113 
     frameEnd    = min(ceil(frameStart+decodeDuration + 0.5*decodeDuration),-globalStart+globalEnd);
90 114
91 
-
92 
-
93 115 
         for iVoxel = 1:nVoxel % linear structure avoids 3D-Loop.
94 
-            % get coordinate for iVoxel
95 
-%             coord =
96 
-
97 
-            % get surrounding coordinates within radius
98 
-%             sphere =
99 
-
100 
-            % calculate decode performance on these coordinates
101 
-            svmdata      = timePointMatrix{index}(:,2:size(timePointMatrix{index},2));
102 
-            svmlabel     = timePointMatrix{index}(:,1);
116 
+            % get surrounding coordinate-IDs within radius
117 
+            sphere = fbs_buildSphere(mapping,iVoxel,radius,vdim);
118 
+
119 
+            %build svm inputmatrix
120 
+            svmdata = [];
121 
+            svmlabel = [];
122 
+            anyvoxel = 1;
123 
+            for pstConditionGroup = 1:size(pst{1,anyvoxel},2)
124 
+                for dp = 1:size(pst{1,anyvoxel}{1,pstConditionGroup},1) % data point
125 
+                    svmlabel = [svmlabel; lm_getSVMLabel(labelMap,eventList(pstConditionGroup,1))];
126 
+                    row = [];
127 
+                    for voxel = 1:size(sphere,2)
128 
+                        row = [row, pst{1,voxel}{1,pstConditionGroup}(dp,frameStart:frameEnd)]; % label,[value,value,...],[value,value,...]...
129 
+                    end
130 
+                    svmdata  = [svmdata; row];
131 
+                end
132 
+            end
103 133
104 134 
             if RANDOMIZE_DATAPOINTS
105 135 
                 rndindex  = randperm(length(svmlabel));
106 136 
                 svmdata   = svmdata(rndindex,:);
107 137 
                 svmlabel  = svmlabel(rndindex);
108 138 
             end
139 
+
109 140 
             decode = svm_single_crossval(svmlabel,svmdata,svmopts);
110 141 
             % save the decode value to the corresponding coordinate
111 
-        end
112 142
113 
-    display('rastering done');
114 
-    % save data for timeslice
143 
+            coord= mapping.indexToCoordMap.get(iVoxel);
144 
+            img3D(coord',timeShift) = decode;
145 
+
146 
+        end  %for each voxel
147 
+
148 
+        nii = make_nii(img3D,vdim,[],16,'decode'); %default origin
149 
+        save_nii(nii,sprintf('TESTFILE%g',timeShift));
115 150
116 151 
     end %for each timeslice
152 
+    display('rastering done');
153 
+elapsed.decode = toc;
154 
+
117 155
118 156 
     clear pst; %save memory!
157 
+assignin('base','timing',elapsed);
119 158 
 end
120 159
121 160 
 end
122 161