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save_untouch0_nii_hdr.m
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save_untouch0_nii_hdr.m
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% internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function save_nii_hdr(hdr, fid)
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
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 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');
fwrite(fid, hk.hkey_un0(1), 'uchar');
return; % header_key
%---------------------------------------------------------------------
function image_dimension(fid, dime)
%struct image_dimension
% { /* off + size */
% short int dim[8]; /* 0 + 16 */
% char vox_units[4]; /* 16 + 4 */
% char cal_units[8]; /* 20 + 8 */
% short int unused1; /* 28 + 2 */
% short int datatype; /* 30 + 2 */
% short int bitpix; /* 32 + 2 */
% 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
% ..etc
% */
% float vox_offset; /* 68 + 4 */
% float roi_scale; /* 72 + 4 */
% float funused1; /* 76 + 4 */
% float funused2; /* 80 + 4 */
% float cal_max; /* 84 + 4 */
% float cal_min; /* 88 + 4 */
% int compressed; /* 92 + 4 */
% int verified; /* 96 + 4 */
% int glmax; /* 100 + 4 */
% int glmin; /* 104 + 4 */
% }; /* total=108 bytes */
fwrite(fid, dime.dim(1:8), 'int16');
pad = zeros(1, 4-length(dime.vox_units));
dime.vox_units = [dime.vox_units char(pad)];
fwrite(fid, dime.vox_units(1:4), 'uchar');
pad = zeros(1, 8-length(dime.cal_units));
dime.cal_units = [dime.cal_units char(pad)];
fwrite(fid, dime.cal_units(1:8), 'uchar');
fwrite(fid, dime.unused1(1), 'int16');
fwrite(fid, dime.datatype(1), 'int16');
fwrite(fid, dime.bitpix(1), 'int16');
fwrite(fid, dime.dim_un0(1), 'int16');
fwrite(fid, dime.pixdim(1:8), 'float32');
fwrite(fid, dime.vox_offset(1), 'float32');
fwrite(fid, dime.roi_scale(1), 'float32');
fwrite(fid, dime.funused1(1), 'float32');
fwrite(fid, dime.funused2(1), 'float32');
fwrite(fid, dime.cal_max(1), 'float32');
fwrite(fid, dime.cal_min(1), 'float32');
fwrite(fid, dime.compressed(1), 'int32');
fwrite(fid, dime.verified(1), 'int32');
fwrite(fid, dime.glmax(1), 'int32');
fwrite(fid, dime.glmin(1), 'int32');
return; % image_dimension
%---------------------------------------------------------------------
function data_history(fid, hist)
% Original header structures - ANALYZE 7.5
%struct data_history
% { /* off + size */
% char descrip[80]; /* 0 + 80 */
% char aux_file[24]; /* 80 + 24 */
% char orient; /* 104 + 1 */
% char originator[10]; /* 105 + 10 */
% char generated[10]; /* 115 + 10 */
% char scannum[10]; /* 125 + 10 */
% char patient_id[10]; /* 135 + 10 */
% char exp_date[10]; /* 145 + 10 */
% char exp_time[10]; /* 155 + 10 */
% char hist_un0[3]; /* 165 + 3 */
% int views /* 168 + 4 */
% int vols_added; /* 172 + 4 */
% int start_field; /* 176 + 4 */
% int field_skip; /* 180 + 4 */
% int omax; /* 184 + 4 */
% int omin; /* 188 + 4 */
% int smax; /* 192 + 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.orient(1), 'uchar');
fwrite(fid, hist.originator(1:5), 'int16');
pad = zeros(1, 10-length(hist.generated));
hist.generated = [hist.generated char(pad)];
fwrite(fid, hist.generated(1:10), 'uchar');
pad = zeros(1, 10-length(hist.scannum));
hist.scannum = [hist.scannum char(pad)];
fwrite(fid, hist.scannum(1:10), 'uchar');
pad = zeros(1, 10-length(hist.patient_id));
hist.patient_id = [hist.patient_id char(pad)];
fwrite(fid, hist.patient_id(1:10), 'uchar');
pad = zeros(1, 10-length(hist.exp_date));
hist.exp_date = [hist.exp_date char(pad)];
fwrite(fid, hist.exp_date(1:10), 'uchar');
pad = zeros(1, 10-length(hist.exp_time));
hist.exp_time = [hist.exp_time char(pad)];
fwrite(fid, hist.exp_time(1:10), 'uchar');
pad = zeros(1, 3-length(hist.hist_un0));
hist.hist_un0 = [hist.hist_un0 char(pad)];
fwrite(fid, hist.hist_un0(1:3), 'uchar');
fwrite(fid, hist.views(1), 'int32');
fwrite(fid, hist.vols_added(1), 'int32');
fwrite(fid, hist.start_field(1),'int32');
fwrite(fid, hist.field_skip(1), 'int32');
fwrite(fid, hist.omax(1), 'int32');
fwrite(fid, hist.omin(1), 'int32');
fwrite(fid, hist.smax(1), 'int32');
fwrite(fid, hist.smin(1), 'int32');
return; % data_history