-
Notifications
You must be signed in to change notification settings - Fork 5
/
avw_hdr_read.m
389 lines (348 loc) · 15.9 KB
/
avw_hdr_read.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
function [ avw, machine ] = avw_hdr_read(fileprefix, machine, verbose)
% avw_hdr_read - read Analyze format data header (*.hdr)
%
% [ avw, machine ] = avw_hdr_read(fileprefix, [machine], [verbose])
%
% fileprefix - string filename (without .hdr); the file name
% can be given as a full path or relative to the
% current directory.
%
% machine - a string, see machineformat in fread for details.
% The default here is 'ieee-le' but the routine
% will automatically switch between little and big
% endian to read any such Analyze header. It
% reports the appropriate machine format and can
% return the machine value.
%
% avw.hdr - a struct, all fields returned from the header.
% For details, find a good description on the web
% or see the Analyze File Format pdf in the
% mri_toolbox doc folder or read this .m file.
%
% verbose - the default is to output processing information to the command
% window. If verbose = 0, this will not happen.
%
% This function is called by avw_img_read
%
% See also avw_hdr_write, avw_hdr_make, avw_view_hdr, avw_view
%
% $Revision: 1.1 $ $Date: 2004/11/12 01:30:25 $
% Licence: GNU GPL, no express or implied warranties
% History: 05/2002, [email protected]
% The Analyze format and c code below is copyright
% (c) Copyright, 1986-1995
% Biomedical Imaging Resource, Mayo Foundation
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~exist('verbose','var'), verbose = 1; end
if verbose,
version = '[$Revision: 1.1 $]';
fprintf('\nAVW_HDR_READ [v%s]\n',version(12:16)); tic;
end
if ~exist('fileprefix','var'),
msg = sprintf('...no input fileprefix - see help avw_hdr_read\n\n');
error(msg);
end
if ~exist('machine','var'), machine = 'ieee-le'; end
if findstr('.hdr',fileprefix),
% fprintf('...removing .hdr extension from ''%s''\n',fileprefix);
fileprefix = strrep(fileprefix,'.hdr','');
end
if findstr('.img',fileprefix),
% fprintf('...removing .img extension from ''%s''\n',fileprefix);
fileprefix = strrep(fileprefix,'.img','');
end
file = sprintf('%s.hdr',fileprefix);
if exist(file),
if verbose,
fprintf('...reading %s Analyze format',machine);
end
fid = fopen(file,'r',machine);
avw.hdr = read_header(fid,verbose);
avw.fileprefix = fileprefix;
fclose(fid);
if ~isequal(avw.hdr.hk.sizeof_hdr,348),
if verbose, fprintf('...failed.\n'); end
% first try reading the opposite endian to 'machine'
switch machine,
case 'ieee-le', machine = 'ieee-be';
case 'ieee-be', machine = 'ieee-le';
end
if verbose, fprintf('...reading %s Analyze format',machine); end
fid = fopen(file,'r',machine);
avw.hdr = read_header(fid,verbose);
avw.fileprefix = fileprefix;
fclose(fid);
end
if ~isequal(avw.hdr.hk.sizeof_hdr,348),
% Now throw an error
if verbose, fprintf('...failed.\n'); end
msg = sprintf('...size of header not equal to 348 bytes!\n\n');
error(msg);
end
else
msg = sprintf('...cannot find file %s.hdr\n\n',file);
error(msg);
end
if verbose,
t=toc; fprintf('...done (%5.2f sec).\n',t);
end
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [ dsr ] = read_header(fid,verbose)
% Original header structures - ANALYZE 7.5
%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,verbose);
dsr.hist = data_history(fid);
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [hk] = header_key(fid)
% The required elements in the header_key substructure are:
%
% int sizeof_header Must indicate the byte size of the header file.
% int extents Should be 16384, the image file is created as
% contiguous with a minimum extent size.
% char regular Must be 'r' to indicate that all images and
% volumes are the same size.
% 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');
hk.sizeof_hdr = fread(fid, 1,'*int32'); % should be 348!
hk.data_type = fread(fid,10,'*char')';
hk.db_name = fread(fid,18,'*char')';
hk.extents = fread(fid, 1,'*int32');
hk.session_error = fread(fid, 1,'*int16');
hk.regular = fread(fid, 1,'*char')'; % might be uint8
hk.hkey_un0 = fread(fid, 1,'*uint8')';
% check if this value was a char zero
if hk.hkey_un0 == 48,
hk.hkey_un0 = 0;
end
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [ dime ] = image_dimension(fid,verbose)
%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
% */
% 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, mm
% pixdim[2] - voxel height, mm
% pixdim[3] - slice thickness, mm
% pixdim[4] - volume timing, in msec
% ..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 */
dime.dim = fread(fid,8,'*int16')';
dime.vox_units = fread(fid,4,'*char')';
dime.cal_units = fread(fid,8,'*char')';
dime.unused1 = fread(fid,1,'*int16');
dime.datatype = fread(fid,1,'*int16');
dime.bitpix = fread(fid,1,'*int16');
dime.dim_un0 = fread(fid,1,'*int16');
dime.pixdim = fread(fid,8,'*float')';
dime.vox_offset = fread(fid,1,'*float');
dime.roi_scale = fread(fid,1,'*float');
dime.funused1 = fread(fid,1,'*float');
dime.funused2 = fread(fid,1,'*float');
dime.cal_max = fread(fid,1,'*float');
dime.cal_min = fread(fid,1,'*float');
dime.compressed = fread(fid,1,'*int32');
dime.verified = fread(fid,1,'*int32');
dime.glmax = fread(fid,1,'*int32');
dime.glmin = fread(fid,1,'*int32');
if dime.dim(1) < 4, % Number of dimensions in database; usually 4.
if verbose,
fprintf('...ensuring 4 dimensions in avw.hdr.dime.dim\n');
end
dime.dim(1) = int16(4);
end
if dime.dim(5) < 1, % Time points; number of volumes in database
if verbose,
fprintf('...ensuring at least 1 volume in avw.hdr.dime.dim(5)\n');
end
dime.dim(5) = int16(1);
end
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [ hist ] = data_history(fid)
% 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 */
hist.descrip = fread(fid,80,'*char')';
hist.aux_file = fread(fid,24,'*char')';
hist.orient = fread(fid, 1,'*uint8'); % see note below on char
hist.originator = fread(fid,10,'*char')';
hist.generated = fread(fid,10,'*char')';
hist.scannum = fread(fid,10,'*char')';
hist.patient_id = fread(fid,10,'*char')';
hist.exp_date = fread(fid,10,'*char')';
hist.exp_time = fread(fid,10,'*char')';
hist.hist_un0 = fread(fid, 3,'*char')';
hist.views = fread(fid, 1,'*int32');
hist.vols_added = fread(fid, 1,'*int32');
hist.start_field = fread(fid, 1,'*int32');
hist.field_skip = fread(fid, 1,'*int32');
hist.omax = fread(fid, 1,'*int32');
hist.omin = fread(fid, 1,'*int32');
hist.smax = fread(fid, 1,'*int32');
hist.smin = fread(fid, 1,'*int32');
% check if hist.orient was saved as ascii char value
switch hist.orient,
case 48, hist.orient = uint8(0);
case 49, hist.orient = uint8(1);
case 50, hist.orient = uint8(2);
case 51, hist.orient = uint8(3);
case 52, hist.orient = uint8(4);
case 53, hist.orient = uint8(5);
end
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 <[email protected]>
% Comments
% The header format is flexible and can be extended for new
% user-defined data types. The essential structures of the header
% are the header_key and the image_dimension.
%
% The required elements in the header_key substructure are:
%
% int sizeof_header Must indicate the byte size of the header file.
% int extents Should be 16384, the image file is created as
% contiguous with a minimum extent size.
% char regular Must be 'r' to indicate that all images and
% volumes are the same size.
%
% The image_dimension substructure describes the organization and
% size of the images. These elements enable the database to reference
% images by volume and slice number. Explanation of each element follows:
%
% short int dim[ ]; /* Array of the image dimensions */
%
% 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.
% dim[5] Undocumented.
% dim[6] Undocumented.
% dim[7] Undocumented.
%
% char vox_units[4] Specifies the spatial units of measure for a voxel.
% char cal_units[8] Specifies the name of the calibration unit.
% short int unused1 /* Unused */
% short int datatype /* Datatype for this image set */
% /*Acceptable values for datatype are*/
% #define DT_NONE 0
% #define DT_UNKNOWN 0 /*Unknown data type*/
% #define DT_BINARY 1 /*Binary ( 1 bit per voxel)*/
% #define DT_UNSIGNED_CHAR 2 /*Unsigned character ( 8 bits per voxel)*/
% #define DT_SIGNED_SHORT 4 /*Signed short (16 bits per voxel)*/
% #define DT_SIGNED_INT 8 /*Signed integer (32 bits per voxel)*/
% #define DT_FLOAT 16 /*Floating point (32 bits per voxel)*/
% #define DT_COMPLEX 32 /*Complex (64 bits per voxel; 2 floating point numbers)/*
% #define DT_DOUBLE 64 /*Double precision (64 bits per voxel)*/
% #define DT_RGB 128 /*A Red-Green-Blue datatype*/
% #define DT_ALL 255 /*Undocumented*/
%
% short int bitpix; /* Number of bits per pixel; 1, 8, 16, 32, or 64. */
% short int dim_un0; /* Unused */
%
% float pixdim[]; Parallel array to dim[], giving real world measurements in mm and ms.
% pixdim[0]; Pixel dimensions?
% pixdim[1]; Voxel width in mm.
% pixdim[2]; Voxel height in mm.
% pixdim[3]; Slice thickness in mm.
% pixdim[4]; timeslice in ms (ie, TR in fMRI).
% pixdim[5]; Undocumented.
% pixdim[6]; Undocumented.
% pixdim[7]; Undocumented.
%
% float vox_offset; Byte offset in the .img file at which voxels start. This value can be
% negative to specify that the absolute value is applied for every image
% in the file.
%
% float roi_scale; Specifies the Region Of Interest scale?
% float funused1; Undocumented.
% float funused2; Undocumented.
%
% float cal_max; Specifies the upper bound of the range of calibration values.
% float cal_min; Specifies the lower bound of the range of calibration values.
%
% int compressed; Undocumented.
% int verified; Undocumented.
%
% int glmax; The maximum pixel value for the entire database.
% int glmin; The minimum pixel value for the entire database.
%
%