/
load_nii_hdr.m
280 lines (233 loc) · 10 KB
/
load_nii_hdr.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
% internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function [hdr, filetype, fileprefix, machine] = load_nii_hdr(fileprefix)
if ~exist('fileprefix','var'),
error('Usage: [hdr, filetype, fileprefix, machine] = load_nii_hdr(filename)');
end
machine = 'ieee-le';
new_ext = 0;
if findstr('.nii',fileprefix)
new_ext = 1;
fileprefix = strrep(fileprefix,'.nii','');
end
if findstr('.hdr',fileprefix)
fileprefix = strrep(fileprefix,'.hdr','');
end
if findstr('.img',fileprefix)
fileprefix = strrep(fileprefix,'.img','');
end
if new_ext
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');
if fread(fid,1,'int32') == 348
hdr = read_header(fid);
fclose(fid);
else
fclose(fid);
% first try reading the opposite endian to 'machine'
%
switch machine,
case 'ieee-le', machine = 'ieee-be';
case 'ieee-be', machine = 'ieee-le';
end
fid = fopen(fn,'r',machine);
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
else
fseek(fid,0,'bof');
if fread(fid,1,'int32') ~= 348
% Now throw an error
%
msg = sprintf('File "%s" is corrupted.',fn);
error(msg);
end
hdr = read_header(fid);
fclose(fid);
end
end
end
if strcmp(hdr.hist.magic, 'n+1')
filetype = 2;
elseif strcmp(hdr.hist.magic, 'ni1')
filetype = 1;
else
filetype = 0;
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)');
fseek(fid,253,'bof');
hist.originator = fread(fid, 5,'int16')';
return % data_history