% internal function % - Jimmy Shen (jimmy@rotman-baycrest.on.ca) function hdr = load_nii_hdr(fileprefix, machine, filetype) if filetype == 2 fn = sprintf('%s.nii',fileprefix); if ~exist(fn) msg = sprintf('Cannot find file "%s.nii".', fileprefix); error(msg); end else fn = sprintf('%s.hdr',fileprefix); if ~exist(fn) msg = sprintf('Cannot find file "%s.hdr".', fileprefix); error(msg); end end fid = fopen(fn,'r',machine); if fid < 0, msg = sprintf('Cannot open file %s.',fn); error(msg); else fseek(fid,0,'bof'); hdr = read_header(fid); fclose(fid); end return % load_nii_hdr %--------------------------------------------------------------------- function [ dsr ] = read_header(fid) % Original header structures % struct dsr % { % struct header_key hk; /* 0 + 40 */ % struct image_dimension dime; /* 40 + 108 */ % struct data_history hist; /* 148 + 200 */ % }; /* total= 348 bytes*/ dsr.hk = header_key(fid); dsr.dime = image_dimension(fid); dsr.hist = data_history(fid); % For Analyze data format % if ~strcmp(dsr.hist.magic, 'n+1') & ~strcmp(dsr.hist.magic, 'ni1') dsr.hist.qform_code = 0; dsr.hist.sform_code = 0; end return % read_header %--------------------------------------------------------------------- function [ hk ] = header_key(fid) 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 */ % % int sizeof_header Should be 348. % char regular Must be 'r' to indicate that all images and % volumes are the same size. v6 = version; if str2num(v6(1))<6 directchar = '*char'; else directchar = 'uchar=>char'; end hk.sizeof_hdr = fread(fid, 1,'int32')'; % should be 348! hk.data_type = deblank(fread(fid,10,directchar)'); hk.db_name = deblank(fread(fid,18,directchar)'); hk.extents = fread(fid, 1,'int32')'; hk.session_error = fread(fid, 1,'int16')'; hk.regular = fread(fid, 1,directchar)'; hk.dim_info = fread(fid, 1,'uchar')'; return % header_key %--------------------------------------------------------------------- function [ dime ] = image_dimension(fid) % Original header structures % struct image_dimension % { /* off + size */ % short int dim[8]; /* 0 + 16 */ % /* % dim[0] Number of dimensions in database; usually 4. % dim[1] Image X dimension; number of *pixels* in an image row. % dim[2] Image Y dimension; number of *pixel rows* in slice. % dim[3] Volume Z dimension; number of *slices* in a volume. % dim[4] Time points; number of volumes in database % */ % 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, mm % pixdim[2] - voxel height, mm % pixdim[3] - slice thickness, mm % 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 */ dime.dim = fread(fid,8,'int16')'; dime.intent_p1 = fread(fid,1,'float32')'; dime.intent_p2 = fread(fid,1,'float32')'; dime.intent_p3 = fread(fid,1,'float32')'; dime.intent_code = fread(fid,1,'int16')'; dime.datatype = fread(fid,1,'int16')'; dime.bitpix = fread(fid,1,'int16')'; dime.slice_start = fread(fid,1,'int16')'; dime.pixdim = fread(fid,8,'float32')'; dime.vox_offset = fread(fid,1,'float32')'; dime.scl_slope = fread(fid,1,'float32')'; dime.scl_inter = fread(fid,1,'float32')'; dime.slice_end = fread(fid,1,'int16')'; dime.slice_code = fread(fid,1,'uchar')'; dime.xyzt_units = fread(fid,1,'uchar')'; dime.cal_max = fread(fid,1,'float32')'; dime.cal_min = fread(fid,1,'float32')'; dime.slice_duration = fread(fid,1,'float32')'; dime.toffset = fread(fid,1,'float32')'; dime.glmax = fread(fid,1,'int32')'; dime.glmin = fread(fid,1,'int32')'; return % image_dimension %--------------------------------------------------------------------- function [ hist ] = data_history(fid) % 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 */ v6 = version; if str2num(v6(1))<6 directchar = '*char'; else directchar = 'uchar=>char'; end hist.descrip = deblank(fread(fid,80,directchar)'); hist.aux_file = deblank(fread(fid,24,directchar)'); hist.qform_code = fread(fid,1,'int16')'; hist.sform_code = fread(fid,1,'int16')'; hist.quatern_b = fread(fid,1,'float32')'; hist.quatern_c = fread(fid,1,'float32')'; hist.quatern_d = fread(fid,1,'float32')'; hist.qoffset_x = fread(fid,1,'float32')'; hist.qoffset_y = fread(fid,1,'float32')'; hist.qoffset_z = fread(fid,1,'float32')'; hist.srow_x = fread(fid,4,'float32')'; hist.srow_y = fread(fid,4,'float32')'; hist.srow_z = fread(fid,4,'float32')'; hist.intent_name = deblank(fread(fid,16,directchar)'); hist.magic = deblank(fread(fid,4,directchar)'); return % data_history