Load NIFTI dataset header. Support both *.nii and *.hdr/*.img file
extension. If file extension is not provided, *.hdr/*.img will be
used as default.
Usage: [hdr, filetype, fileprefix, machine] = load_nii_hdr_cbi(filename)
filename - NIFTI file name.
Returned values:
hdr - struct with NIFTI header fields.
filetype - 0 for Analyze format (*.hdr/*.img);
1 for NIFTI format in 2 files (*.hdr/*.img);
2 for NIFTI format in 1 file (*.nii).
fileprefix - NIFTI file name without extension.
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.
Number of scanned images in the file can be obtained by:
num_scan = hdr.dime.dim(5)
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 (pls@rotman-baycrest.on.ca)0001 % Load NIFTI dataset header. Support both *.nii and *.hdr/*.img file 0002 % extension. If file extension is not provided, *.hdr/*.img will be 0003 % used as default. 0004 % 0005 % Usage: [hdr, filetype, fileprefix, machine] = load_nii_hdr_cbi(filename) 0006 % 0007 % filename - NIFTI file name. 0008 % 0009 % Returned values: 0010 % 0011 % hdr - struct with NIFTI header fields. 0012 % 0013 % filetype - 0 for Analyze format (*.hdr/*.img); 0014 % 1 for NIFTI format in 2 files (*.hdr/*.img); 0015 % 2 for NIFTI format in 1 file (*.nii). 0016 % 0017 % fileprefix - NIFTI file name without extension. 0018 % 0019 % machine - a string, see below for details. The default here is 'ieee-le'. 0020 % 0021 % 'native' or 'n' - local machine format - the default 0022 % 'ieee-le' or 'l' - IEEE floating point with little-endian 0023 % byte ordering 0024 % 'ieee-be' or 'b' - IEEE floating point with big-endian 0025 % byte ordering 0026 % 'vaxd' or 'd' - VAX D floating point and VAX ordering 0027 % 'vaxg' or 'g' - VAX G floating point and VAX ordering 0028 % 'cray' or 'c' - Cray floating point with big-endian 0029 % byte ordering 0030 % 'ieee-le.l64' or 'a' - IEEE floating point with little-endian 0031 % byte ordering and 64 bit long data type 0032 % 'ieee-be.l64' or 's' - IEEE floating point with big-endian byte 0033 % ordering and 64 bit long data type. 0034 % 0035 % Number of scanned images in the file can be obtained by: 0036 % num_scan = hdr.dime.dim(5) 0037 % 0038 % Part of this file is copied and modified under GNU license from 0039 % MRI_TOOLBOX developed by CNSP in Flinders University, Australia 0040 % 0041 % NIFTI data format can be found on: http://nifti.nimh.nih.gov 0042 % 0043 % - Jimmy Shen (pls@rotman-baycrest.on.ca) 0044 % 0045 function [hdr, filetype, fileprefix, machine] = load_nii_hdr_cbi(fileprefix) 0046 0047 if ~exist('fileprefix','var'), 0048 error('Usage: [hdr, filetype, fileprefix, machine] = load_nii_hdr_cbi(filename)'); 0049 end 0050 0051 if ~exist('machine','var'), machine = 'ieee-le'; end 0052 0053 new_ext = 0; 0054 0055 if findstr('.nii',fileprefix) 0056 new_ext = 1; 0057 fileprefix = strrep(fileprefix,'.nii',''); 0058 end 0059 0060 if findstr('.hdr',fileprefix) 0061 fileprefix = strrep(fileprefix,'.hdr',''); 0062 end 0063 0064 if findstr('.img',fileprefix) 0065 fileprefix = strrep(fileprefix,'.img',''); 0066 end 0067 0068 if new_ext 0069 fn = sprintf('%s.nii',fileprefix); 0070 0071 if ~exist(fn) 0072 msg = sprintf('Cannot find file "%s.nii".', fileprefix); 0073 error(msg); 0074 end 0075 else 0076 fn = sprintf('%s.hdr',fileprefix); 0077 0078 if ~exist(fn) 0079 msg = sprintf('Cannot find file "%s.hdr".', fileprefix); 0080 error(msg); 0081 end 0082 end 0083 0084 % rhayashi added encoding 0085 fid = fopen_ascii_encoding(fn, 'r', machine); 0086 0087 if fid < 0, 0088 msg = sprintf('Cannot open file %s.',fn); 0089 error(msg); 0090 else 0091 hdr = read_header(fid); 0092 fclose(fid); 0093 end 0094 0095 if hdr.hk.sizeof_hdr ~= 348 0096 % first try reading the opposite endian to 'machine' 0097 switch machine, 0098 case 'ieee-le', machine = 'ieee-be'; 0099 case 'ieee-be', machine = 'ieee-le'; 0100 end 0101 0102 % rhayashi added encoding 0103 fid = fopen_ascii_encoding(fn, 'r', machine); 0104 0105 if fid < 0, 0106 msg = sprintf('Cannot open file %s.',fn); 0107 error(msg); 0108 else 0109 hdr = read_header(fid); 0110 fclose(fid); 0111 end 0112 end 0113 0114 if hdr.hk.sizeof_hdr ~= 348 0115 % Now throw an error 0116 msg = sprintf('File "%s" is corrupted.',fn); 0117 error(msg); 0118 end 0119 0120 if strcmp(hdr.hist.magic, 'n+1') 0121 filetype = 2; 0122 elseif strcmp(hdr.hist.magic, 'ni1') 0123 filetype = 1; 0124 else 0125 filetype = 0; 0126 end 0127 0128 return % load_nii_hdr_cbi 0129 0130 function [ fid ] = fopen_ascii_encoding(file, mode, machine) 0131 0132 if vb_matlab_version('>=', '7.2') 0133 fid = fopen(file, mode, machine, 'US-ASCII'); 0134 else 0135 fid = fopen(file, mode, machine); 0136 end 0137 0138 %--------------------------------------------------------------------- 0139 function [ dsr ] = read_header(fid) 0140 0141 % Original header structures 0142 % struct dsr 0143 % { 0144 % struct header_key hk; /* 0 + 40 */ 0145 % struct image_dimension dime; /* 40 + 108 */ 0146 % struct data_history hist; /* 148 + 200 */ 0147 % }; /* total= 348 bytes*/ 0148 0149 dsr.hk = header_key(fid); 0150 dsr.dime = image_dimension(fid); 0151 dsr.hist = data_history(fid); 0152 0153 % For Analyze data format 0154 % 0155 if ~strcmp(dsr.hist.magic, 'n+1') & ~strcmp(dsr.hist.magic, 'ni1') 0156 dsr.hist.qform_code = 0; 0157 dsr.hist.sform_code = 0; 0158 end 0159 0160 return % read_header 0161 0162 0163 %--------------------------------------------------------------------- 0164 function [ hk ] = header_key(fid) 0165 0166 fseek(fid,0,'bof'); 0167 0168 % Original header structures 0169 % struct header_key /* header key */ 0170 % { /* off + size */ 0171 % int sizeof_hdr /* 0 + 4 */ 0172 % char data_type[10]; /* 4 + 10 */ 0173 % char db_name[18]; /* 14 + 18 */ 0174 % int extents; /* 32 + 4 */ 0175 % short int session_error; /* 36 + 2 */ 0176 % char regular; /* 38 + 1 */ 0177 % char dim_info; % char hkey_un0; /* 39 + 1 */ 0178 % }; /* total=40 bytes */ 0179 % 0180 % int sizeof_header Should be 348. 0181 % char regular Must be 'r' to indicate that all images and 0182 % volumes are the same size. 0183 0184 hk.sizeof_hdr = fread(fid, 1,'int32')'; % should be 348! 0185 hk.data_type = deblank(fread(fid,10,'*char')'); 0186 hk.db_name = deblank(fread(fid,18,'*char')'); 0187 hk.extents = fread(fid, 1,'int32')'; 0188 hk.session_error = fread(fid, 1,'int16')'; 0189 hk.regular = fread(fid, 1,'*char')'; 0190 hk.dim_info = fread(fid, 1,'char')'; 0191 0192 return % header_key 0193 0194 0195 %--------------------------------------------------------------------- 0196 function [ dime ] = image_dimension(fid) 0197 0198 % Original header structures 0199 % struct image_dimension 0200 % { /* off + size */ 0201 % short int dim[8]; /* 0 + 16 */ 0202 % /* 0203 % dim[0] Number of dimensions in database; usually 4. 0204 % dim[1] Image X dimension; number of *pixels* in an image row. 0205 % dim[2] Image Y dimension; number of *pixel rows* in slice. 0206 % dim[3] Volume Z dimension; number of *slices* in a volume. 0207 % dim[4] Time points; number of volumes in database 0208 % */ 0209 % float intent_p1; % char vox_units[4]; /* 16 + 4 */ 0210 % float intent_p2; % char cal_units[8]; /* 20 + 4 */ 0211 % float intent_p3; % char cal_units[8]; /* 24 + 4 */ 0212 % short int intent_code; % short int unused1; /* 28 + 2 */ 0213 % short int datatype; /* 30 + 2 */ 0214 % short int bitpix; /* 32 + 2 */ 0215 % short int slice_start; % short int dim_un0; /* 34 + 2 */ 0216 % float pixdim[8]; /* 36 + 32 */ 0217 % /* 0218 % pixdim[] specifies the voxel dimensions: 0219 % pixdim[1] - voxel width, mm 0220 % pixdim[2] - voxel height, mm 0221 % pixdim[3] - slice thickness, mm 0222 % pixdim[4] - volume timing, in msec 0223 % ..etc 0224 % */ 0225 % float vox_offset; /* 68 + 4 */ 0226 % float scl_slope; % float roi_scale; /* 72 + 4 */ 0227 % float scl_inter; % float funused1; /* 76 + 4 */ 0228 % short slice_end; % float funused2; /* 80 + 2 */ 0229 % char slice_code; % float funused2; /* 82 + 1 */ 0230 % char xyzt_units; % float funused2; /* 83 + 1 */ 0231 % float cal_max; /* 84 + 4 */ 0232 % float cal_min; /* 88 + 4 */ 0233 % float slice_duration; % int compressed; /* 92 + 4 */ 0234 % float toffset; % int verified; /* 96 + 4 */ 0235 % int glmax; /* 100 + 4 */ 0236 % int glmin; /* 104 + 4 */ 0237 % }; /* total=108 bytes */ 0238 0239 dime.dim = fread(fid,8,'int16')'; 0240 dime.intent_p1 = fread(fid,1,'float32')'; 0241 dime.intent_p2 = fread(fid,1,'float32')'; 0242 dime.intent_p3 = fread(fid,1,'float32')'; 0243 dime.intent_code = fread(fid,1,'int16')'; 0244 dime.datatype = fread(fid,1,'int16')'; 0245 dime.bitpix = fread(fid,1,'int16')'; 0246 dime.slice_start = fread(fid,1,'int16')'; 0247 dime.pixdim = fread(fid,8,'float32')'; 0248 dime.vox_offset = fread(fid,1,'float32')'; 0249 dime.scl_slope = fread(fid,1,'float32')'; 0250 dime.scl_inter = fread(fid,1,'float32')'; 0251 dime.slice_end = fread(fid,1,'int16')'; 0252 dime.slice_code = fread(fid,1,'char')'; 0253 dime.xyzt_units = fread(fid,1,'char')'; 0254 dime.cal_max = fread(fid,1,'float32')'; 0255 dime.cal_min = fread(fid,1,'float32')'; 0256 dime.slice_duration = fread(fid,1,'float32')'; 0257 dime.toffset = fread(fid,1,'float32')'; 0258 dime.glmax = fread(fid,1,'int32')'; 0259 dime.glmin = fread(fid,1,'int32')'; 0260 0261 return % image_dimension 0262 0263 0264 %--------------------------------------------------------------------- 0265 function [ hist ] = data_history(fid) 0266 0267 % Original header structures 0268 % struct data_history 0269 % { /* off + size */ 0270 % char descrip[80]; /* 0 + 80 */ 0271 % char aux_file[24]; /* 80 + 24 */ 0272 % short int qform_code; /* 104 + 2 */ 0273 % short int sform_code; /* 106 + 2 */ 0274 % float quatern_b; /* 108 + 4 */ 0275 % float quatern_c; /* 112 + 4 */ 0276 % float quatern_d; /* 116 + 4 */ 0277 % float qoffset_x; /* 120 + 4 */ 0278 % float qoffset_y; /* 124 + 4 */ 0279 % float qoffset_z; /* 128 + 4 */ 0280 % float srow_x[4]; /* 132 + 16 */ 0281 % float srow_y[4]; /* 148 + 16 */ 0282 % float srow_z[4]; /* 164 + 16 */ 0283 % char intent_name[16]; /* 180 + 16 */ 0284 % char magic[4]; % int smin; /* 196 + 4 */ 0285 % }; /* total=200 bytes */ 0286 0287 hist.descrip = deblank(fread(fid,80,'*char')'); 0288 hist.aux_file = deblank(fread(fid,24,'*char')'); 0289 hist.qform_code = fread(fid,1,'int16')'; 0290 hist.sform_code = fread(fid,1,'int16')'; 0291 hist.quatern_b = fread(fid,1,'float32')'; 0292 hist.quatern_c = fread(fid,1,'float32')'; 0293 hist.quatern_d = fread(fid,1,'float32')'; 0294 hist.qoffset_x = fread(fid,1,'float32')'; 0295 hist.qoffset_y = fread(fid,1,'float32')'; 0296 hist.qoffset_z = fread(fid,1,'float32')'; 0297 hist.srow_x = fread(fid,4,'float32')'; 0298 hist.srow_y = fread(fid,4,'float32')'; 0299 hist.srow_z = fread(fid,4,'float32')'; 0300 hist.intent_name = deblank(fread(fid,16,'*char')'); 0301 hist.magic = deblank(fread(fid,4,'*char')'); 0302 0303 fseek(fid,253,'bof'); 0304 hist.originator = fread(fid, 5,'int16')'; 0305 0306 return % data_history 0307