/
save_nii_hdr.m
227 lines (188 loc) · 9.27 KB
/
save_nii_hdr.m
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% internal function
% - 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