% Save NIFTI dataset header. Support both *.nii and *.hdr/*.img file % extension. % % Usage: save_nii_hdr(hdr, fid) % % hdr - struct with NIFTI header fields. % % fileprefix - NIFTI file name without extension. % % Part of this file is copied and modified under GNU license from % MRI_TOOLBOX developed by CNSP in Flinders University, Australia % % NIFTI data format can be found on: http://nifti.nimh.nih.gov % % - Jimmy Shen (jimmy@rotman-baycrest.on.ca) % function save_nii_hdr(hdr, fid) if ~exist('hdr','var') | ~exist('fid','var') error('Usage: save_nii_hdr(hdr, fid)'); end if ~isequal(hdr.hk.sizeof_hdr,348), error('hdr.hk.sizeof_hdr must be 348.'); end if hdr.hist.qform_code == 0 & hdr.hist.sform_code == 0 hdr.hist.sform_code = 1; hdr.hist.srow_x(1) = hdr.dime.pixdim(2); hdr.hist.srow_x(2) = 0; hdr.hist.srow_x(3) = 0; hdr.hist.srow_y(1) = 0; hdr.hist.srow_y(2) = hdr.dime.pixdim(3); hdr.hist.srow_y(3) = 0; hdr.hist.srow_z(1) = 0; hdr.hist.srow_z(2) = 0; hdr.hist.srow_z(3) = hdr.dime.pixdim(4); hdr.hist.srow_x(4) = (1-hdr.hist.originator(1))*hdr.dime.pixdim(2); hdr.hist.srow_y(4) = (1-hdr.hist.originator(2))*hdr.dime.pixdim(3); hdr.hist.srow_z(4) = (1-hdr.hist.originator(3))*hdr.dime.pixdim(4); end write_header(hdr, fid); return; % save_nii_hdr %--------------------------------------------------------------------- function write_header(hdr, fid) % Original header structures % struct dsr /* dsr = hdr */ % { % struct header_key hk; /* 0 + 40 */ % struct image_dimension dime; /* 40 + 108 */ % struct data_history hist; /* 148 + 200 */ % }; /* total= 348 bytes*/ header_key(fid, hdr.hk); image_dimension(fid, hdr.dime); data_history(fid, hdr.hist); % check the file size is 348 bytes % fbytes = ftell(fid); if ~isequal(fbytes,348), msg = sprintf('Header size is not 348 bytes.'); warning(msg); end return; % write_header %--------------------------------------------------------------------- function header_key(fid, hk) fseek(fid,0,'bof'); % Original header structures % struct header_key /* header key */ % { /* off + size */ % int sizeof_hdr /* 0 + 4 */ % char data_type[10]; /* 4 + 10 */ % char db_name[18]; /* 14 + 18 */ % int extents; /* 32 + 4 */ % short int session_error; /* 36 + 2 */ % char regular; /* 38 + 1 */ % char dim_info; % char hkey_un0; /* 39 + 1 */ % }; /* total=40 bytes */ fwrite(fid, hk.sizeof_hdr(1), 'int32'); % must be 348. % data_type = sprintf('%-10s',hk.data_type); % ensure it is 10 chars from left % fwrite(fid, data_type(1:10), 'uchar'); pad = zeros(1, 10-length(hk.data_type)); hk.data_type = [hk.data_type char(pad)]; fwrite(fid, hk.data_type(1:10), 'uchar'); % db_name = sprintf('%-18s', hk.db_name); % ensure it is 18 chars from left % fwrite(fid, db_name(1:18), 'uchar'); pad = zeros(1, 18-length(hk.db_name)); hk.db_name = [hk.db_name char(pad)]; fwrite(fid, hk.db_name(1:18), 'uchar'); fwrite(fid, hk.extents(1), 'int32'); fwrite(fid, hk.session_error(1), 'int16'); fwrite(fid, hk.regular(1), 'uchar'); % might be uint8 % fwrite(fid, hk.hkey_un0(1), 'uchar'); % fwrite(fid, hk.hkey_un0(1), 'uint8'); fwrite(fid, hk.dim_info(1), 'uchar'); return; % header_key %--------------------------------------------------------------------- function image_dimension(fid, dime) % Original header structures % struct image_dimension % { /* off + size */ % short int dim[8]; /* 0 + 16 */ % float intent_p1; % char vox_units[4]; /* 16 + 4 */ % float intent_p2; % char cal_units[8]; /* 20 + 4 */ % float intent_p3; % char cal_units[8]; /* 24 + 4 */ % short int intent_code; % short int unused1; /* 28 + 2 */ % short int datatype; /* 30 + 2 */ % short int bitpix; /* 32 + 2 */ % short int slice_start; % short int dim_un0; /* 34 + 2 */ % float pixdim[8]; /* 36 + 32 */ % /* % pixdim[] specifies the voxel dimensions: % pixdim[1] - voxel width % pixdim[2] - voxel height % pixdim[3] - interslice distance % pixdim[4] - volume timing, in msec % ..etc % */ % float vox_offset; /* 68 + 4 */ % float scl_slope; % float roi_scale; /* 72 + 4 */ % float scl_inter; % float funused1; /* 76 + 4 */ % short slice_end; % float funused2; /* 80 + 2 */ % char slice_code; % float funused2; /* 82 + 1 */ % char xyzt_units; % float funused2; /* 83 + 1 */ % float cal_max; /* 84 + 4 */ % float cal_min; /* 88 + 4 */ % float slice_duration; % int compressed; /* 92 + 4 */ % float toffset; % int verified; /* 96 + 4 */ % int glmax; /* 100 + 4 */ % int glmin; /* 104 + 4 */ % }; /* total=108 bytes */ fwrite(fid, dime.dim(1:8), 'int16'); fwrite(fid, dime.intent_p1(1), 'float32'); fwrite(fid, dime.intent_p2(1), 'float32'); fwrite(fid, dime.intent_p3(1), 'float32'); fwrite(fid, dime.intent_code(1), 'int16'); fwrite(fid, dime.datatype(1), 'int16'); fwrite(fid, dime.bitpix(1), 'int16'); fwrite(fid, dime.slice_start(1), 'int16'); fwrite(fid, dime.pixdim(1:8), 'float32'); fwrite(fid, dime.vox_offset(1), 'float32'); fwrite(fid, dime.scl_slope(1), 'float32'); fwrite(fid, dime.scl_inter(1), 'float32'); fwrite(fid, dime.slice_end(1), 'int16'); fwrite(fid, dime.slice_code(1), 'uchar'); fwrite(fid, dime.xyzt_units(1), 'uchar'); fwrite(fid, dime.cal_max(1), 'float32'); fwrite(fid, dime.cal_min(1), 'float32'); fwrite(fid, dime.slice_duration(1), 'float32'); fwrite(fid, dime.toffset(1), 'float32'); fwrite(fid, dime.glmax(1), 'int32'); fwrite(fid, dime.glmin(1), 'int32'); return; % image_dimension %--------------------------------------------------------------------- function data_history(fid, hist) % Original header structures %struct data_history % { /* off + size */ % char descrip[80]; /* 0 + 80 */ % char aux_file[24]; /* 80 + 24 */ % short int qform_code; /* 104 + 2 */ % short int sform_code; /* 106 + 2 */ % float quatern_b; /* 108 + 4 */ % float quatern_c; /* 112 + 4 */ % float quatern_d; /* 116 + 4 */ % float qoffset_x; /* 120 + 4 */ % float qoffset_y; /* 124 + 4 */ % float qoffset_z; /* 128 + 4 */ % float srow_x[4]; /* 132 + 16 */ % float srow_y[4]; /* 148 + 16 */ % float srow_z[4]; /* 164 + 16 */ % char intent_name[16]; /* 180 + 16 */ % char magic[4]; % int smin; /* 196 + 4 */ % }; /* total=200 bytes */ % descrip = sprintf('%-80s', hist.descrip); % 80 chars from left % fwrite(fid, descrip(1:80), 'uchar'); pad = zeros(1, 80-length(hist.descrip)); hist.descrip = [hist.descrip char(pad)]; fwrite(fid, hist.descrip(1:80), 'uchar'); % aux_file = sprintf('%-24s', hist.aux_file); % 24 chars from left % fwrite(fid, aux_file(1:24), 'uchar'); pad = zeros(1, 24-length(hist.aux_file)); hist.aux_file = [hist.aux_file char(pad)]; fwrite(fid, hist.aux_file(1:24), 'uchar'); fwrite(fid, hist.qform_code, 'int16'); fwrite(fid, hist.sform_code, 'int16'); fwrite(fid, hist.quatern_b, 'float32'); fwrite(fid, hist.quatern_c, 'float32'); fwrite(fid, hist.quatern_d, 'float32'); fwrite(fid, hist.qoffset_x, 'float32'); fwrite(fid, hist.qoffset_y, 'float32'); fwrite(fid, hist.qoffset_z, 'float32'); fwrite(fid, hist.srow_x(1:4), 'float32'); fwrite(fid, hist.srow_y(1:4), 'float32'); fwrite(fid, hist.srow_z(1:4), 'float32'); % intent_name = sprintf('%-16s', hist.intent_name); % 16 chars from left % fwrite(fid, intent_name(1:16), 'uchar'); pad = zeros(1, 16-length(hist.intent_name)); hist.intent_name = [hist.intent_name char(pad)]; fwrite(fid, hist.intent_name(1:16), 'uchar'); % magic = sprintf('%-4s', hist.magic); % 4 chars from left % fwrite(fid, magic(1:4), 'uchar'); pad = zeros(1, 4-length(hist.magic)); hist.magic = [hist.magic char(pad)]; fwrite(fid, hist.magic(1:4), 'uchar'); return; % data_history