NIFTI_20090325/load_untouch_nii.m (87b08fd) - SVMCrossVal.git

load_untouch_nii.m

%  Load NIFTI or ANALYZE dataset, but not applying any appropriate affine
%  geometric transform or voxel intensity scaling.
%
%  Although according to NIFTI website, all those header information are
%  supposed to be applied to the loaded NIFTI image, there are some
%  situations that people do want to leave the original NIFTI header and
%  data untouched. They will probably just use MATLAB to do certain image
%  processing regardless of image orientation, and to save data back with
%  the same NIfTI header.
%
%  Since this program is only served for those situations, please use it
%  together with "save_untouch_nii.m", and do not use "save_nii.m" or
%  "view_nii.m" for the data that is loaded by "load_untouch_nii.m". For
%  normal situation, you should use "load_nii.m" instead.
%  
%  Usage: nii = load_untouch_nii(filename, [img_idx], [dim5_idx], [dim6_idx], [dim7_idx])
%  
%  filename  - 	NIFTI or ANALYZE file name.
%  
%  img_idx (optional)  -  a numerical array of image volume indices.
%	Only the specified volumes will be loaded. All available image
%	volumes will be loaded, if it is default or empty.
%
%	The number of images scans can be obtained from get_nii_frame.m,
%	or simply: hdr.dime.dim(5).
%
%  dim5_idx (optional)  -  a numerical array of 5th dimension indices.
%	Only the specified range will be loaded. All available range
%	will be loaded, if it is default or empty.
%
%  dim6_idx (optional)  -  a numerical array of 6th dimension indices.
%	Only the specified range will be loaded. All available range
%	will be loaded, if it is default or empty.
%
%  dim7_idx (optional)  -  a numerical array of 7th dimension indices.
%	Only the specified range will be loaded. All available range
%	will be loaded, if it is default or empty.
%
%  Returned values:
%  
%  nii structure:
%
%	hdr -		struct with NIFTI header fields.
%
%	filetype -	Analyze format .hdr/.img (0); 
%			NIFTI .hdr/.img (1);
%			NIFTI .nii (2)
%
%	fileprefix - 	NIFTI filename without extension.
%
%	machine - 	machine string variable.
%
%	img - 		3D (or 4D) matrix of NIFTI data.
%
%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
function nii = load_untouch_nii(filename, img_idx, dim5_idx, dim6_idx, dim7_idx)

if ~exist('filename','var')
      error('Usage: nii = load_untouch_nii(filename, [img_idx], [dim5_idx], [dim6_idx], [dim7_idx])');
   end

if ~exist('img_idx','var') | isempty(img_idx)
      img_idx = [];
   end

if ~exist('dim5_idx','var') | isempty(dim5_idx)
      dim5_idx = [];
   end

if ~exist('dim6_idx','var') | isempty(dim6_idx)
      dim6_idx = [];
   end

if ~exist('dim7_idx','var') | isempty(dim7_idx)
      dim7_idx = [];
   end

%  Read the dataset header
   %
   [nii.hdr,nii.filetype,nii.fileprefix,nii.machine] = load_nii_hdr(filename);

if nii.filetype == 0
      nii.hdr = load_untouch0_nii_hdr(nii.fileprefix,nii.machine);
      nii.ext = [];
   else
      nii.hdr = load_untouch_nii_hdr(nii.fileprefix,nii.machine,nii.filetype);

%  Read the header extension
      %
      nii.ext = load_nii_ext(filename);
   end

%  Read the dataset body
   %
   [nii.img,nii.hdr] = load_nii_img(nii.hdr,nii.filetype,nii.fileprefix, ...
		nii.machine,img_idx,dim5_idx,dim6_idx,dim7_idx);

%  Perform some of sform/qform transform
   %
%   nii = xform_nii(nii, tolerance, preferredForm);

nii.untouch = 1;

return					% load_untouch_nii

SVMCrossVal.git

searchlight ready. missing nifti-image-write support. added timing to FBS