% Write Analyze format header file (*.hdr) % % rri_avw_hdr_write(avw, fileprefix, [machine]) % % avw - a struct with .hdr field, which itself is a struct, % containing all fields of an Analyze header. % % fileprefix - a string, the filename without the .hdr extension. % If empty, may use avw.fileprefix. the file name % can be given as a full path or relative to the % current directory. % % machine - a string, see below for details. The default here is 'ieee-le'. % % 'native' or 'n' - local machine format - the default % 'ieee-le' or 'l' - IEEE floating point with little-endian % byte ordering % 'ieee-be' or 'b' - IEEE floating point with big-endian % byte ordering % 'vaxd' or 'd' - VAX D floating point and VAX ordering % 'vaxg' or 'g' - VAX G floating point and VAX ordering % 'cray' or 'c' - Cray floating point with big-endian % byte ordering % 'ieee-le.l64' or 'a' - IEEE floating point with little-endian % byte ordering and 64 bit long data type % 'ieee-be.l64' or 's' - IEEE floating point with big-endian byte % ordering and 64 bit long data type. % % % Part (or all) of this file is copied and modified under GNU license % from MRI_TOOLBOX developed by CNSP in Flinders University, Australia % function rri_avw_hdr_write(avw, fileprefix, machine) if ~exist('avw','var'), %fprintf('...no input avw - calling avw_hdr_make\n'); avw = avw_hdr_make; elseif isempty(avw), %fprintf('...empty input avw - calling avw_hdr_make\n'); avw = avw_hdr_make; elseif ~isfield(avw,'hdr'), %fprintf('...empty input avw.hdr - calling avw_hdr_make\n'); avw = avw_hdr_make; end if ~isequal(avw.hdr.hk.sizeof_hdr,348), msg = sprintf('...avw.hdr.hk.sizeof_hdr must be 348!\n'); error(msg); end quit = 0; if ~exist('fileprefix','var'), if isfield(avw,'fileprefix'), if ~isempty(avw.fileprefix), fileprefix = avw.fileprefix; else, quit = 1; end else quit = 1; end if quit, %fprintf('...no input fileprefix - see help avw_hdr_write\n\n'); helpwin avw_hdr_write; return; end end if ~exist('machine','var'), machine = 'ieee-le'; end if findstr('.hdr',fileprefix), % %fprintf('AVW_HDR_WRITE: Removing .hdr extension from ''%s''\n',fileprefix); fileprefix = strrep(fileprefix,'.hdr',''); end %---------------------------------------------------------------------------- % MAIN tic; fid = fopen(sprintf('%s.hdr',fileprefix),'w',machine); if fid < 0, msg = sprintf('Cannot write to file %s.hdr\n',fileprefix); error(msg); else %fprintf('...writing %s Analyze header.\n',machine); write_header(fid,avw); end %t=toc; %fprintf('...done (%5.2f sec).\n\n',t); return %---------------------------------------------------------------------------- function write_header(fid,avw) header_key(fid,avw.hdr.hk); image_dimension( fid, avw.hdr.dime, max(avw.img(:)), min(avw.img(:)) ); data_history(fid,avw.hdr.hist); % check the file size is 348 bytes fbytes = ftell(fid); fclose(fid); if ~isequal(fbytes,348), msg = sprintf('...file size is not 348 bytes!\n'); warning(msg); end return %---------------------------------------------------------------------------- function header_key(fid,hk) % Original header structures - ANALYZE 7.5 % 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 */ fseek(fid,0,'bof'); fwrite(fid, hk.sizeof_hdr(1), 'int32'); % must be 348! data_type = sprintf('%-10s',hk.data_type); % ensure it is 10 chars fwrite(fid, hk.data_type(1:10), 'uchar'); db_name = sprintf('%-18s',hk.db_name); % ensure it is 18 chars fwrite(fid, db_name(1:18), 'uchar'); fwrite(fid, hk.extents(1), 'int32'); fwrite(fid, hk.session_error(1),'int16'); regular = sprintf('%1s',hk.regular); % ensure it is 1 char fwrite(fid, regular(1), 'uchar'); % might be uint8 %hkey_un0 = sprintf('%1s',hk.hkey_un0); % ensure it is 1 char %fwrite(fid, hkey_un0(1), 'uchar'); fwrite(fid, hk.hkey_un0(1), 'uint8'); % >Would you set hkey_un0 as char or uint8? % Really doesn't make any difference. As far as anyone here can remember, % this was just to pad to an even byte boundary for that structure. I guess % I'd suggest setting it to a uint8 value of 0 (i.e, truly zero-valued) so % that it doesn't look like anything important! % Denny return %---------------------------------------------------------------------------- function image_dimension(fid,dime,maxval,minval) %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'); fwrite(fid, dime.vox_units(1:4),'uchar'); 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'); % Ensure compatibility with SPM (according to MRIcro) if dime.roi_scale == 0, dime.roi_scale = 0.00392157; end 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'); fwrite(fid, maxval, 'int32'); fwrite(fid, minval, 'int32'); return %---------------------------------------------------------------------------- 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 aux_file = sprintf('%-24s', hist.aux_file); % 24 chars % originator = sprintf('%-10s', hist.originator); % 10 chars generated = sprintf('%-10s', hist.generated); % 10 chars scannum = sprintf('%-10s', hist.scannum); % 10 chars patient_id = sprintf('%-10s', hist.patient_id); % 10 chars exp_date = sprintf('%-10s', hist.exp_date); % 10 chars exp_time = sprintf('%-10s', hist.exp_time); % 10 chars hist_un0 = sprintf( '%-3s', hist.hist_un0); % 3 chars fwrite(fid, descrip(1:80), 'uchar'); fwrite(fid, aux_file(1:24), 'uchar'); %orient = sprintf( '%1s', hist.orient); % 1 char %fwrite(fid, orient(1), 'uchar'); fwrite(fid, hist.orient(1), 'uint8'); % see note below on char % Using 'int16[5]' instead of 'char[10]' is to make % sure the compatibility with SPM to read/write origin % % fwrite(fid, originator(1:10), 'uchar'); fwrite(fid, hist.originator(1:5), 'int16'); fwrite(fid, generated(1:10), 'uchar'); fwrite(fid, scannum(1:10), 'uchar'); fwrite(fid, patient_id(1:10), 'uchar'); fwrite(fid, exp_date(1:10), 'uchar'); fwrite(fid, exp_time(1:10), 'uchar'); fwrite(fid, 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 % Note on using char: % The 'char orient' field in the header is intended to % hold simply an 8-bit unsigned integer value, not the ASCII representation % of the character for that value. A single 'char' byte is often used to % represent an integer value in Analyze if the known value range doesn't % go beyond 0-255 - saves a byte over a short int, which may not mean % much in today's computing environments, but given that this format % has been around since the early 1980's, saving bytes here and there on % older systems was important! In this case, 'char' simply provides the % byte of storage - not an indicator of the format for what is stored in % this byte. Generally speaking, anytime a single 'char' is used, it is % probably meant to hold an 8-bit integer value, whereas if this has % been dimensioned as an array, then it is intended to hold an ASCII % character string, even if that was only a single character. % Denny % See other notes in avw_hdr_read