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niftilib
nifti1.h
Go to the documentation of this file.
1
12
#ifndef _NIFTI_HEADER_
13
#define _NIFTI_HEADER_
14
15
/*****************************************************************************
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** This file defines the "NIFTI-1" header format. **
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** It is derived from 2 meetings at the NIH (31 Mar 2003 and **
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** 02 Sep 2003) of the Data Format Working Group (DFWG), **
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** chartered by the NIfTI (Neuroimaging Informatics Technology **
20
** Initiative) at the National Institutes of Health (NIH). **
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**--------------------------------------------------------------**
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** Neither the National Institutes of Health (NIH), the DFWG, **
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** nor any of the members or employees of these institutions **
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** imply any warranty of usefulness of this material for any **
25
** purpose, and do not assume any liability for damages, **
26
** incidental or otherwise, caused by any use of this document. **
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** If these conditions are not acceptable, do not use this! **
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**--------------------------------------------------------------**
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** Author: Robert W Cox (NIMH, Bethesda) **
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** Advisors: John Ashburner (FIL, London), **
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** Stephen Smith (FMRIB, Oxford), **
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** Mark Jenkinson (FMRIB, Oxford) **
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******************************************************************************/
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35
/*---------------------------------------------------------------------------*/
36
/* Note that the ANALYZE 7.5 file header (dbh.h) is
37
(c) Copyright 1986-1995
38
Biomedical Imaging Resource
39
Mayo Foundation
40
Incorporation of components of dbh.h are by permission of the
41
Mayo Foundation.
42
43
Changes from the ANALYZE 7.5 file header in this file are released to the
44
public domain, including the functional comments and any amusing asides.
45
-----------------------------------------------------------------------------*/
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47
/*---------------------------------------------------------------------------*/
115
/*---------------------------------------------------------------------------*/
116
/* HEADER STRUCT DECLARATION:
117
-------------------------
118
In the comments below for each field, only NIFTI-1 specific requirements
119
or changes from the ANALYZE 7.5 format are described. For convenience,
120
the 348 byte header is described as a single struct, rather than as the
121
ANALYZE 7.5 group of 3 substructs.
122
123
Further comments about the interpretation of various elements of this
124
header are after the data type definition itself. Fields that are
125
marked as ++UNUSED++ have no particular interpretation in this standard.
126
(Also see the UNUSED FIELDS comment section, far below.)
127
128
The presumption below is that the various C types have particular sizes:
129
sizeof(int) = sizeof(float) = 4 ; sizeof(short) = 2
130
-----------------------------------------------------------------------------*/
131
132
/*=================*/
133
#ifdef __cplusplus
134
extern
"C"
{
135
#endif
136
/*=================*/
137
143
/*************************/
/************************/
144
struct
nifti_1_header
{
/* NIFTI-1 usage */
/* ANALYZE 7.5 field(s) */
145
/*************************/
/************************/
146
147
/*--- was header_key substruct ---*/
148
int
sizeof_hdr
;
/* int sizeof_hdr; */
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char
data_type
[10];
/* char data_type[10]; */
150
char
db_name
[18];
/* char db_name[18]; */
151
int
extents
;
/* int extents; */
152
short
session_error
;
/* short session_error; */
153
char
regular
;
/* char regular; */
154
char
dim_info
;
/* char hkey_un0; */
155
156
/*--- was image_dimension substruct ---*/
157
short
dim
[8];
/* short dim[8]; */
158
float
intent_p1
;
/* short unused8; */
159
/* short unused9; */
160
float
intent_p2
;
/* short unused10; */
161
/* short unused11; */
162
float
intent_p3
;
/* short unused12; */
163
/* short unused13; */
164
short
intent_code
;
/* short unused14; */
165
short
datatype
;
/* short datatype; */
166
short
bitpix
;
/* short bitpix; */
167
short
slice_start
;
/* short dim_un0; */
168
float
pixdim
[8];
/* float pixdim[8]; */
169
float
vox_offset
;
/* float vox_offset; */
170
float
scl_slope
;
/* float funused1; */
171
float
scl_inter
;
/* float funused2; */
172
short
slice_end
;
/* float funused3; */
173
char
slice_code
;
174
char
xyzt_units
;
175
float
cal_max
;
/* float cal_max; */
176
float
cal_min
;
/* float cal_min; */
177
float
slice_duration
;
/* float compressed; */
178
float
toffset
;
/* float verified; */
179
int
glmax
;
/* int glmax; */
180
int
glmin
;
/* int glmin; */
181
182
/*--- was data_history substruct ---*/
183
char
descrip
[80];
/* char descrip[80]; */
184
char
aux_file
[24];
/* char aux_file[24]; */
185
186
short
qform_code
;
/*-- all ANALYZE 7.5 ---*/
187
short
sform_code
;
/* fields below here */
188
/* are replaced */
189
float
quatern_b
;
190
float
quatern_c
;
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float
quatern_d
;
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float
qoffset_x
;
193
float
qoffset_y
;
194
float
qoffset_z
;
196
float
srow_x
[4] ;
197
float
srow_y
[4] ;
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float
srow_z
[4] ;
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char
intent_name
[16];
202
char
magic
[4] ;
204
} ;
/**** 348 bytes total ****/
205
206
typedef
struct
nifti_1_header
nifti_1_header
;
207
208
/*---------------------------------------------------------------------------*/
209
/* HEADER EXTENSIONS:
210
-----------------
211
After the end of the 348 byte header (e.g., after the magic field),
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the next 4 bytes are a char array field named "extension". By default,
213
all 4 bytes of this array should be set to zero. In a .nii file, these
214
4 bytes will always be present, since the earliest start point for
215
the image data is byte #352. In a separate .hdr file, these bytes may
216
or may not be present. If not present (i.e., if the length of the .hdr
217
file is 348 bytes), then a NIfTI-1 compliant program should use the
218
default value of extension={0,0,0,0}. The first byte (extension[0])
219
is the only value of this array that is specified at present. The other
220
3 bytes are reserved for future use.
221
222
If extension[0] is nonzero, it indicates that extended header information
223
is present in the bytes following the extension array. In a .nii file,
224
this extended header data is before the image data (and vox_offset
225
must be set correctly to allow for this). In a .hdr file, this extended
226
data follows extension and proceeds (potentially) to the end of the file.
227
228
The format of extended header data is weakly specified. Each extension
229
must be an integer multiple of 16 bytes long. The first 8 bytes of each
230
extension comprise 2 integers:
231
int esize , ecode ;
232
These values may need to be byte-swapped, as indicated by dim[0] for
233
the rest of the header.
234
* esize is the number of bytes that form the extended header data
235
+ esize must be a positive integral multiple of 16
236
+ this length includes the 8 bytes of esize and ecode themselves
237
* ecode is a non-negative integer that indicates the format of the
238
extended header data that follows
239
+ different ecode values are assigned to different developer groups
240
+ at present, the "registered" values for code are
241
= 0 = unknown private format (not recommended!)
242
= 2 = DICOM format (i.e., attribute tags and values)
243
= 4 = AFNI group (i.e., ASCII XML-ish elements)
244
In the interests of interoperability (a primary rationale for NIfTI),
245
groups developing software that uses this extension mechanism are
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encouraged to document and publicize the format of their extensions.
247
To this end, the NIfTI DFWG will assign even numbered codes upon request
248
to groups submitting at least rudimentary documentation for the format
249
of their extension; at present, the contact is mailto:rwcox@nih.gov.
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The assigned codes and documentation will be posted on the NIfTI
251
website. All odd values of ecode (and 0) will remain unassigned;
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at least, until the even ones are used up, when we get to 2,147,483,646.
253
254
Note that the other contents of the extended header data section are
255
totally unspecified by the NIfTI-1 standard. In particular, if binary
256
data is stored in such a section, its byte order is not necessarily
257
the same as that given by examining dim[0]; it is incumbent on the
258
programs dealing with such data to determine the byte order of binary
259
extended header data.
260
261
Multiple extended header sections are allowed, each starting with an
262
esize,ecode value pair. The first esize value, as described above,
263
is at bytes #352-355 in the .hdr or .nii file (files start at byte #0).
264
If this value is positive, then the second (esize2) will be found
265
starting at byte #352+esize1 , the third (esize3) at byte #352+esize1+esize2,
266
et cetera. Of course, in a .nii file, the value of vox_offset must
267
be compatible with these extensions. If a malformed file indicates
268
that an extended header data section would run past vox_offset, then
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the entire extended header section should be ignored. In a .hdr file,
270
if an extended header data section would run past the end-of-file,
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that extended header data should also be ignored.
272
273
With the above scheme, a program can successively examine the esize
274
and ecode values, and skip over each extended header section if the
275
program doesn't know how to interpret the data within. Of course, any
276
program can simply ignore all extended header sections simply by jumping
277
straight to the image data using vox_offset.
278
-----------------------------------------------------------------------------*/
279
287
struct
nifti1_extender
{
char
extension[4] ; } ;
288
typedef
struct
nifti1_extender
nifti1_extender
;
289
293
struct
nifti1_extension
{
294
int
esize
;
295
int
ecode
;
296
char
*
edata
;
297
} ;
298
typedef
struct
nifti1_extension
nifti1_extension
;
299
300
/*---------------------------------------------------------------------------*/
301
/* DATA DIMENSIONALITY (as in ANALYZE 7.5):
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---------------------------------------
303
dim[0] = number of dimensions;
304
- if dim[0] is outside range 1..7, then the header information
305
needs to be byte swapped appropriately
306
- ANALYZE supports dim[0] up to 7, but NIFTI-1 reserves
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dimensions 1,2,3 for space (x,y,z), 4 for time (t), and
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5,6,7 for anything else needed.
309
310
dim[i] = length of dimension #i, for i=1..dim[0] (must be positive)
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- also see the discussion of intent_code, far below
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pixdim[i] = voxel width along dimension #i, i=1..dim[0] (positive)
314
- cf. ORIENTATION section below for use of pixdim[0]
315
- the units of pixdim can be specified with the xyzt_units
316
field (also described far below).
317
318
Number of bits per voxel value is in bitpix, which MUST correspond with
319
the datatype field. The total number of bytes in the image data is
320
dim[1] * ... * dim[dim[0]] * bitpix / 8
321
322
In NIFTI-1 files, dimensions 1,2,3 are for space, dimension 4 is for time,
323
and dimension 5 is for storing multiple values at each spatiotemporal
324
voxel. Some examples:
325
- A typical whole-brain FMRI experiment's time series:
326
- dim[0] = 4
327
- dim[1] = 64 pixdim[1] = 3.75 xyzt_units = NIFTI_UNITS_MM
328
- dim[2] = 64 pixdim[2] = 3.75 | NIFTI_UNITS_SEC
329
- dim[3] = 20 pixdim[3] = 5.0
330
- dim[4] = 120 pixdim[4] = 2.0
331
- A typical T1-weighted anatomical volume:
332
- dim[0] = 3
333
- dim[1] = 256 pixdim[1] = 1.0 xyzt_units = NIFTI_UNITS_MM
334
- dim[2] = 256 pixdim[2] = 1.0
335
- dim[3] = 128 pixdim[3] = 1.1
336
- A single slice EPI time series:
337
- dim[0] = 4
338
- dim[1] = 64 pixdim[1] = 3.75 xyzt_units = NIFTI_UNITS_MM
339
- dim[2] = 64 pixdim[2] = 3.75 | NIFTI_UNITS_SEC
340
- dim[3] = 1 pixdim[3] = 5.0
341
- dim[4] = 1200 pixdim[4] = 0.2
342
- A 3-vector stored at each point in a 3D volume:
343
- dim[0] = 5
344
- dim[1] = 256 pixdim[1] = 1.0 xyzt_units = NIFTI_UNITS_MM
345
- dim[2] = 256 pixdim[2] = 1.0
346
- dim[3] = 128 pixdim[3] = 1.1
347
- dim[4] = 1 pixdim[4] = 0.0
348
- dim[5] = 3 intent_code = NIFTI_INTENT_VECTOR
349
- A single time series with a 3x3 matrix at each point:
350
- dim[0] = 5
351
- dim[1] = 1 xyzt_units = NIFTI_UNITS_SEC
352
- dim[2] = 1
353
- dim[3] = 1
354
- dim[4] = 1200 pixdim[4] = 0.2
355
- dim[5] = 9 intent_code = NIFTI_INTENT_GENMATRIX
356
- intent_p1 = intent_p2 = 3.0 (indicates matrix dimensions)
357
-----------------------------------------------------------------------------*/
358
359
/*---------------------------------------------------------------------------*/
360
/* DATA STORAGE:
361
------------
362
If the magic field is "n+1", then the voxel data is stored in the
363
same file as the header. In this case, the voxel data starts at offset
364
(int)vox_offset into the header file. Thus, vox_offset=352.0 means that
365
the data starts immediately after the NIFTI-1 header. If vox_offset is
366
greater than 352, the NIFTI-1 format does not say much about the
367
contents of the dataset file between the end of the header and the
368
start of the data.
369
370
FILES:
371
-----
372
If the magic field is "ni1", then the voxel data is stored in the
373
associated ".img" file, starting at offset 0 (i.e., vox_offset is not
374
used in this case, and should be set to 0.0).
375
376
When storing NIFTI-1 datasets in pairs of files, it is customary to name
377
the files in the pattern "name.hdr" and "name.img", as in ANALYZE 7.5.
378
When storing in a single file ("n+1"), the file name should be in
379
the form "name.nii" (the ".nft" and ".nif" suffixes are already taken;
380
cf. http://www.icdatamaster.com/n.html ).
381
382
BYTE ORDERING:
383
-------------
384
The byte order of the data arrays is presumed to be the same as the byte
385
order of the header (which is determined by examining dim[0]).
386
387
Floating point types are presumed to be stored in IEEE-754 format.
388
-----------------------------------------------------------------------------*/
389
390
/*---------------------------------------------------------------------------*/
391
/* DETAILS ABOUT vox_offset:
392
------------------------
393
In a .nii file, the vox_offset field value is interpreted as the start
394
location of the image data bytes in that file. In a .hdr/.img file pair,
395
the vox_offset field value is the start location of the image data
396
bytes in the .img file.
397
* If vox_offset is less than 352 in a .nii file, it is equivalent
398
to 352 (i.e., image data never starts before byte #352 in a .nii file).
399
* The default value for vox_offset in a .nii file is 352.
400
* In a .hdr file, the default value for vox_offset is 0.
401
* vox_offset should be an integer multiple of 16; otherwise, some
402
programs may not work properly (e.g., SPM). This is to allow
403
memory-mapped input to be properly byte-aligned.
404
Note that since vox_offset is an IEEE-754 32 bit float (for compatibility
405
with the ANALYZE-7.5 format), it effectively has a 24 bit mantissa. All
406
integers from 0 to 2^24 can be represented exactly in this format, but not
407
all larger integers are exactly storable as IEEE-754 32 bit floats. However,
408
unless you plan to have vox_offset be potentially larger than 16 MB, this
409
should not be an issue. (Actually, any integral multiple of 16 up to 2^27
410
can be represented exactly in this format, which allows for up to 128 MB
411
of random information before the image data. If that isn't enough, then
412
perhaps this format isn't right for you.)
413
414
In a .img file (i.e., image data stored separately from the NIfTI-1
415
header), data bytes between #0 and #vox_offset-1 (inclusive) are completely
416
undefined and unregulated by the NIfTI-1 standard. One potential use of
417
having vox_offset > 0 in the .hdr/.img file pair storage method is to make
418
the .img file be a copy of (or link to) a pre-existing image file in some
419
other format, such as DICOM; then vox_offset would be set to the offset of
420
the image data in this file. (It may not be possible to follow the
421
"multiple-of-16 rule" with an arbitrary external file; using the NIfTI-1
422
format in such a case may lead to a file that is incompatible with software
423
that relies on vox_offset being a multiple of 16.)
424
425
In a .nii file, data bytes between #348 and #vox_offset-1 (inclusive) may
426
be used to store user-defined extra information; similarly, in a .hdr file,
427
any data bytes after byte #347 are available for user-defined extra
428
information. The (very weak) regulation of this extra header data is
429
described elsewhere.
430
-----------------------------------------------------------------------------*/
431
432
/*---------------------------------------------------------------------------*/
433
/* DATA SCALING:
434
------------
435
If the scl_slope field is nonzero, then each voxel value in the dataset
436
should be scaled as
437
y = scl_slope * x + scl_inter
438
where x = voxel value stored
439
y = "true" voxel value
440
Normally, we would expect this scaling to be used to store "true" floating
441
values in a smaller integer datatype, but that is not required. That is,
442
it is legal to use scaling even if the datatype is a float type (crazy,
443
perhaps, but legal).
444
- However, the scaling is to be ignored if datatype is DT_RGB24.
445
- If datatype is a complex type, then the scaling is to be
446
applied to both the real and imaginary parts.
447
448
The cal_min and cal_max fields (if nonzero) are used for mapping (possibly
449
scaled) dataset values to display colors:
450
- Minimum display intensity (black) corresponds to dataset value cal_min.
451
- Maximum display intensity (white) corresponds to dataset value cal_max.
452
- Dataset values below cal_min should display as black also, and values
453
above cal_max as white.
454
- Colors "black" and "white", of course, may refer to any scalar display
455
scheme (e.g., a color lookup table specified via aux_file).
456
- cal_min and cal_max only make sense when applied to scalar-valued
457
datasets (i.e., dim[0] < 5 or dim[5] = 1).
458
-----------------------------------------------------------------------------*/
459
460
/*---------------------------------------------------------------------------*/
461
/* TYPE OF DATA (acceptable values for datatype field):
462
---------------------------------------------------
463
Values of datatype smaller than 256 are ANALYZE 7.5 compatible.
464
Larger values are NIFTI-1 additions. These are all multiples of 256, so
465
that no bits below position 8 are set in datatype. But there is no need
466
to use only powers-of-2, as the original ANALYZE 7.5 datatype codes do.
467
468
The additional codes are intended to include a complete list of basic
469
scalar types, including signed and unsigned integers from 8 to 64 bits,
470
floats from 32 to 128 bits, and complex (float pairs) from 64 to 256 bits.
471
472
Note that most programs will support only a few of these datatypes!
473
A NIFTI-1 program should fail gracefully (e.g., print a warning message)
474
when it encounters a dataset with a type it doesn't like.
475
-----------------------------------------------------------------------------*/
476
477
#undef DT_UNKNOWN
/* defined in dirent.h on some Unix systems */
478
483
/*--- the original ANALYZE 7.5 type codes ---*/
484
#define DT_NONE 0
485
#define DT_UNKNOWN 0
/* what it says, dude */
486
#define DT_BINARY 1
/* binary (1 bit/voxel) */
487
#define DT_UNSIGNED_CHAR 2
/* unsigned char (8 bits/voxel) */
488
#define DT_SIGNED_SHORT 4
/* signed short (16 bits/voxel) */
489
#define DT_SIGNED_INT 8
/* signed int (32 bits/voxel) */
490
#define DT_FLOAT 16
/* float (32 bits/voxel) */
491
#define DT_COMPLEX 32
/* complex (64 bits/voxel) */
492
#define DT_DOUBLE 64
/* double (64 bits/voxel) */
493
#define DT_RGB 128
/* RGB triple (24 bits/voxel) */
494
#define DT_ALL 255
/* not very useful (?) */
495
496
/*----- another set of names for the same ---*/
497
#define DT_UINT8 2
498
#define DT_INT16 4
499
#define DT_INT32 8
500
#define DT_FLOAT32 16
501
#define DT_COMPLEX64 32
502
#define DT_FLOAT64 64
503
#define DT_RGB24 128
504
505
/*------------------- new codes for NIFTI ---*/
506
#define DT_INT8 256
/* signed char (8 bits) */
507
#define DT_UINT16 512
/* unsigned short (16 bits) */
508
#define DT_UINT32 768
/* unsigned int (32 bits) */
509
#define DT_INT64 1024
/* long long (64 bits) */
510
#define DT_UINT64 1280
/* unsigned long long (64 bits) */
511
#define DT_FLOAT128 1536
/* long double (128 bits) */
512
#define DT_COMPLEX128 1792
/* double pair (128 bits) */
513
#define DT_COMPLEX256 2048
/* long double pair (256 bits) */
514
#define DT_RGBA32 2304
/* 4 byte RGBA (32 bits/voxel) */
515
/* @} */
516
517
518
/*------- aliases for all the above codes ---*/
519
525
#define NIFTI_TYPE_UINT8 2
526
527
#define NIFTI_TYPE_INT16 4
528
529
#define NIFTI_TYPE_INT32 8
530
531
#define NIFTI_TYPE_FLOAT32 16
532
533
#define NIFTI_TYPE_COMPLEX64 32
534
535
#define NIFTI_TYPE_FLOAT64 64
536
537
#define NIFTI_TYPE_RGB24 128
538
539
#define NIFTI_TYPE_INT8 256
540
541
#define NIFTI_TYPE_UINT16 512
542
543
#define NIFTI_TYPE_UINT32 768
544
545
#define NIFTI_TYPE_INT64 1024
546
547
#define NIFTI_TYPE_UINT64 1280
548
549
#define NIFTI_TYPE_FLOAT128 1536
550
551
#define NIFTI_TYPE_COMPLEX128 1792
552
553
#define NIFTI_TYPE_COMPLEX256 2048
554
555
#define NIFTI_TYPE_RGBA32 2304
556
/* @} */
557
558
/*-------- sample typedefs for complicated types ---*/
559
#if 0
560
typedef
struct
{
float
r,i; } complex_float ;
561
typedef
struct
{
double
r,i; } complex_double ;
562
typedef
struct
{
long
double
r,i; } complex_longdouble ;
563
typedef
struct
{
unsigned
char
r,g,b; } rgb_byte ;
564
#endif
565
566
/*---------------------------------------------------------------------------*/
567
/* INTERPRETATION OF VOXEL DATA:
568
----------------------------
569
The intent_code field can be used to indicate that the voxel data has
570
some particular meaning. In particular, a large number of codes is
571
given to indicate that the the voxel data should be interpreted as
572
being drawn from a given probability distribution.
573
574
VECTOR-VALUED DATASETS:
575
----------------------
576
The 5th dimension of the dataset, if present (i.e., dim[0]=5 and
577
dim[5] > 1), contains multiple values (e.g., a vector) to be stored
578
at each spatiotemporal location. For example, the header values
579
- dim[0] = 5
580
- dim[1] = 64
581
- dim[2] = 64
582
- dim[3] = 20
583
- dim[4] = 1 (indicates no time axis)
584
- dim[5] = 3
585
- datatype = DT_FLOAT
586
- intent_code = NIFTI_INTENT_VECTOR
587
mean that this dataset should be interpreted as a 3D volume (64x64x20),
588
with a 3-vector of floats defined at each point in the 3D grid.
589
590
A program reading a dataset with a 5th dimension may want to reformat
591
the image data to store each voxels' set of values together in a struct
592
or array. This programming detail, however, is beyond the scope of the
593
NIFTI-1 file specification! Uses of dimensions 6 and 7 are also not
594
specified here.
595
596
STATISTICAL PARAMETRIC DATASETS (i.e., SPMs):
597
--------------------------------------------
598
Values of intent_code from NIFTI_FIRST_STATCODE to NIFTI_LAST_STATCODE
599
(inclusive) indicate that the numbers in the dataset should be interpreted
600
as being drawn from a given distribution. Most such distributions have
601
auxiliary parameters (e.g., NIFTI_INTENT_TTEST has 1 DOF parameter).
602
603
If the dataset DOES NOT have a 5th dimension, then the auxiliary parameters
604
are the same for each voxel, and are given in header fields intent_p1,
605
intent_p2, and intent_p3.
606
607
If the dataset DOES have a 5th dimension, then the auxiliary parameters
608
are different for each voxel. For example, the header values
609
- dim[0] = 5
610
- dim[1] = 128
611
- dim[2] = 128
612
- dim[3] = 1 (indicates a single slice)
613
- dim[4] = 1 (indicates no time axis)
614
- dim[5] = 2
615
- datatype = DT_FLOAT
616
- intent_code = NIFTI_INTENT_TTEST
617
mean that this is a 2D dataset (128x128) of t-statistics, with the
618
t-statistic being in the first "plane" of data and the degrees-of-freedom
619
parameter being in the second "plane" of data.
620
621
If the dataset 5th dimension is used to store the voxel-wise statistical
622
parameters, then dim[5] must be 1 plus the number of parameters required
623
by that distribution (e.g., intent_code=NIFTI_INTENT_TTEST implies dim[5]
624
must be 2, as in the example just above).
625
626
Note: intent_code values 2..10 are compatible with AFNI 1.5x (which is
627
why there is no code with value=1, which is obsolescent in AFNI).
628
629
OTHER INTENTIONS:
630
----------------
631
The purpose of the intent_* fields is to help interpret the values
632
stored in the dataset. Some non-statistical values for intent_code
633
and conventions are provided for storing other complex data types.
634
635
The intent_name field provides space for a 15 character (plus 0 byte)
636
'name' string for the type of data stored. Examples:
637
- intent_code = NIFTI_INTENT_ESTIMATE; intent_name = "T1";
638
could be used to signify that the voxel values are estimates of the
639
NMR parameter T1.
640
- intent_code = NIFTI_INTENT_TTEST; intent_name = "House";
641
could be used to signify that the voxel values are t-statistics
642
for the significance of 'activation' response to a House stimulus.
643
- intent_code = NIFTI_INTENT_DISPVECT; intent_name = "ToMNI152";
644
could be used to signify that the voxel values are a displacement
645
vector that transforms each voxel (x,y,z) location to the
646
corresponding location in the MNI152 standard brain.
647
- intent_code = NIFTI_INTENT_SYMMATRIX; intent_name = "DTI";
648
could be used to signify that the voxel values comprise a diffusion
649
tensor image.
650
651
If no data name is implied or needed, intent_name[0] should be set to 0.
652
-----------------------------------------------------------------------------*/
653
656
#define NIFTI_INTENT_NONE 0
657
658
/*-------- These codes are for probability distributions ---------------*/
659
/* Most distributions have a number of parameters,
660
below denoted by p1, p2, and p3, and stored in
661
- intent_p1, intent_p2, intent_p3 if dataset doesn't have 5th dimension
662
- image data array if dataset does have 5th dimension
663
664
Functions to compute with many of the distributions below can be found
665
in the CDF library from U Texas.
666
667
Formulas for and discussions of these distributions can be found in the
668
following books:
669
670
[U] Univariate Discrete Distributions,
671
NL Johnson, S Kotz, AW Kemp.
672
673
[C1] Continuous Univariate Distributions, vol. 1,
674
NL Johnson, S Kotz, N Balakrishnan.
675
676
[C2] Continuous Univariate Distributions, vol. 2,
677
NL Johnson, S Kotz, N Balakrishnan. */
678
/*----------------------------------------------------------------------*/
679
688
#define NIFTI_INTENT_CORREL 2
689
692
#define NIFTI_INTENT_TTEST 3
693
697
#define NIFTI_INTENT_FTEST 4
698
701
#define NIFTI_INTENT_ZSCORE 5
702
706
#define NIFTI_INTENT_CHISQ 6
707
711
#define NIFTI_INTENT_BETA 7
712
717
#define NIFTI_INTENT_BINOM 8
718
723
#define NIFTI_INTENT_GAMMA 9
724
728
#define NIFTI_INTENT_POISSON 10
729
733
#define NIFTI_INTENT_NORMAL 11
734
739
#define NIFTI_INTENT_FTEST_NONC 12
740
744
#define NIFTI_INTENT_CHISQ_NONC 13
745
750
#define NIFTI_INTENT_LOGISTIC 14
751
756
#define NIFTI_INTENT_LAPLACE 15
757
760
#define NIFTI_INTENT_UNIFORM 16
761
765
#define NIFTI_INTENT_TTEST_NONC 17
766
772
#define NIFTI_INTENT_WEIBULL 18
773
780
#define NIFTI_INTENT_CHI 19
781
787
#define NIFTI_INTENT_INVGAUSS 20
788
793
#define NIFTI_INTENT_EXTVAL 21
794
797
#define NIFTI_INTENT_PVAL 22
798
805
#define NIFTI_INTENT_LOGPVAL 23
806
812
#define NIFTI_INTENT_LOG10PVAL 24
813
816
#define NIFTI_FIRST_STATCODE 2
817
820
#define NIFTI_LAST_STATCODE 24
821
822
/*---------- these values for intent_code aren't for statistics ----------*/
823
828
#define NIFTI_INTENT_ESTIMATE 1001
829
834
#define NIFTI_INTENT_LABEL 1002
835
839
#define NIFTI_INTENT_NEURONAME 1003
840
853
#define NIFTI_INTENT_GENMATRIX 1004
854
866
#define NIFTI_INTENT_SYMMATRIX 1005
867
875
#define NIFTI_INTENT_DISPVECT 1006
/* specifically for displacements */
876
#define NIFTI_INTENT_VECTOR 1007
/* for any other type of vector */
877
889
#define NIFTI_INTENT_POINTSET 1008
890
902
#define NIFTI_INTENT_TRIANGLE 1009
903
911
#define NIFTI_INTENT_QUATERNION 1010
912
916
#define NIFTI_INTENT_DIMLESS 1011
917
918
/*---------- these values apply to GIFTI datasets ----------*/
919
922
#define NIFTI_INTENT_TIME_SERIES 2001
923
927
#define NIFTI_INTENT_NODE_INDEX 2002
928
938
#define NIFTI_INTENT_RGB_VECTOR 2003
939
949
#define NIFTI_INTENT_RGBA_VECTOR 2004
950
954
#define NIFTI_INTENT_SHAPE 2005
955
956
/* @} */
957
958
/*---------------------------------------------------------------------------*/
959
/* 3D IMAGE (VOLUME) ORIENTATION AND LOCATION IN SPACE:
960
---------------------------------------------------
961
There are 3 different methods by which continuous coordinates can
962
attached to voxels. The discussion below emphasizes 3D volumes, and
963
the continuous coordinates are referred to as (x,y,z). The voxel
964
index coordinates (i.e., the array indexes) are referred to as (i,j,k),
965
with valid ranges:
966
i = 0 .. dim[1]-1
967
j = 0 .. dim[2]-1 (if dim[0] >= 2)
968
k = 0 .. dim[3]-1 (if dim[0] >= 3)
969
The (x,y,z) coordinates refer to the CENTER of a voxel. In methods
970
2 and 3, the (x,y,z) axes refer to a subject-based coordinate system,
971
with
972
+x = Right +y = Anterior +z = Superior.
973
This is a right-handed coordinate system. However, the exact direction
974
these axes point with respect to the subject depends on qform_code
975
(Method 2) and sform_code (Method 3).
976
977
N.B.: The i index varies most rapidly, j index next, k index slowest.
978
Thus, voxel (i,j,k) is stored starting at location
979
(i + j*dim[1] + k*dim[1]*dim[2]) * (bitpix/8)
980
into the dataset array.
981
982
N.B.: The ANALYZE 7.5 coordinate system is
983
+x = Left +y = Anterior +z = Superior
984
which is a left-handed coordinate system. This backwardness is
985
too difficult to tolerate, so this NIFTI-1 standard specifies the
986
coordinate order which is most common in functional neuroimaging.
987
988
N.B.: The 3 methods below all give the locations of the voxel centers
989
in the (x,y,z) coordinate system. In many cases, programs will wish
990
to display image data on some other grid. In such a case, the program
991
will need to convert its desired (x,y,z) values into (i,j,k) values
992
in order to extract (or interpolate) the image data. This operation
993
would be done with the inverse transformation to those described below.
994
995
N.B.: Method 2 uses a factor 'qfac' which is either -1 or 1; qfac is
996
stored in the otherwise unused pixdim[0]. If pixdim[0]=0.0 (which
997
should not occur), we take qfac=1. Of course, pixdim[0] is only used
998
when reading a NIFTI-1 header, not when reading an ANALYZE 7.5 header.
999
1000
N.B.: The units of (x,y,z) can be specified using the xyzt_units field.
1001
1002
METHOD 1 (the "old" way, used only when qform_code = 0):
1003
-------------------------------------------------------
1004
The coordinate mapping from (i,j,k) to (x,y,z) is the ANALYZE
1005
7.5 way. This is a simple scaling relationship:
1006
1007
x = pixdim[1] * i
1008
y = pixdim[2] * j
1009
z = pixdim[3] * k
1010
1011
No particular spatial orientation is attached to these (x,y,z)
1012
coordinates. (NIFTI-1 does not have the ANALYZE 7.5 orient field,
1013
which is not general and is often not set properly.) This method
1014
is not recommended, and is present mainly for compatibility with
1015
ANALYZE 7.5 files.
1016
1017
METHOD 2 (used when qform_code > 0, which should be the "normal" case):
1018
---------------------------------------------------------------------
1019
The (x,y,z) coordinates are given by the pixdim[] scales, a rotation
1020
matrix, and a shift. This method is intended to represent
1021
"scanner-anatomical" coordinates, which are often embedded in the
1022
image header (e.g., DICOM fields (0020,0032), (0020,0037), (0028,0030),
1023
and (0018,0050)), and represent the nominal orientation and location of
1024
the data. This method can also be used to represent "aligned"
1025
coordinates, which would typically result from some post-acquisition
1026
alignment of the volume to a standard orientation (e.g., the same
1027
subject on another day, or a rigid rotation to true anatomical
1028
orientation from the tilted position of the subject in the scanner).
1029
The formula for (x,y,z) in terms of header parameters and (i,j,k) is:
1030
1031
[ x ] [ R11 R12 R13 ] [ pixdim[1] * i ] [ qoffset_x ]
1032
[ y ] = [ R21 R22 R23 ] [ pixdim[2] * j ] + [ qoffset_y ]
1033
[ z ] [ R31 R32 R33 ] [ qfac * pixdim[3] * k ] [ qoffset_z ]
1034
1035
The qoffset_* shifts are in the NIFTI-1 header. Note that the center
1036
of the (i,j,k)=(0,0,0) voxel (first value in the dataset array) is
1037
just (x,y,z)=(qoffset_x,qoffset_y,qoffset_z).
1038
1039
The rotation matrix R is calculated from the quatern_* parameters.
1040
This calculation is described below.
1041
1042
The scaling factor qfac is either 1 or -1. The rotation matrix R
1043
defined by the quaternion parameters is "proper" (has determinant 1).
1044
This may not fit the needs of the data; for example, if the image
1045
grid is
1046
i increases from Left-to-Right
1047
j increases from Anterior-to-Posterior
1048
k increases from Inferior-to-Superior
1049
Then (i,j,k) is a left-handed triple. In this example, if qfac=1,
1050
the R matrix would have to be
1051
1052
[ 1 0 0 ]
1053
[ 0 -1 0 ] which is "improper" (determinant = -1).
1054
[ 0 0 1 ]
1055
1056
If we set qfac=-1, then the R matrix would be
1057
1058
[ 1 0 0 ]
1059
[ 0 -1 0 ] which is proper.
1060
[ 0 0 -1 ]
1061
1062
This R matrix is represented by quaternion [a,b,c,d] = [0,1,0,0]
1063
(which encodes a 180 degree rotation about the x-axis).
1064
1065
METHOD 3 (used when sform_code > 0):
1066
-----------------------------------
1067
The (x,y,z) coordinates are given by a general affine transformation
1068
of the (i,j,k) indexes:
1069
1070
x = srow_x[0] * i + srow_x[1] * j + srow_x[2] * k + srow_x[3]
1071
y = srow_y[0] * i + srow_y[1] * j + srow_y[2] * k + srow_y[3]
1072
z = srow_z[0] * i + srow_z[1] * j + srow_z[2] * k + srow_z[3]
1073
1074
The srow_* vectors are in the NIFTI_1 header. Note that no use is
1075
made of pixdim[] in this method.
1076
1077
WHY 3 METHODS?
1078
--------------
1079
Method 1 is provided only for backwards compatibility. The intention
1080
is that Method 2 (qform_code > 0) represents the nominal voxel locations
1081
as reported by the scanner, or as rotated to some fiducial orientation and
1082
location. Method 3, if present (sform_code > 0), is to be used to give
1083
the location of the voxels in some standard space. The sform_code
1084
indicates which standard space is present. Both methods 2 and 3 can be
1085
present, and be useful in different contexts (method 2 for displaying the
1086
data on its original grid; method 3 for displaying it on a standard grid).
1087
1088
In this scheme, a dataset would originally be set up so that the
1089
Method 2 coordinates represent what the scanner reported. Later,
1090
a registration to some standard space can be computed and inserted
1091
in the header. Image display software can use either transform,
1092
depending on its purposes and needs.
1093
1094
In Method 2, the origin of coordinates would generally be whatever
1095
the scanner origin is; for example, in MRI, (0,0,0) is the center
1096
of the gradient coil.
1097
1098
In Method 3, the origin of coordinates would depend on the value
1099
of sform_code; for example, for the Talairach coordinate system,
1100
(0,0,0) corresponds to the Anterior Commissure.
1101
1102
QUATERNION REPRESENTATION OF ROTATION MATRIX (METHOD 2)
1103
-------------------------------------------------------
1104
The orientation of the (x,y,z) axes relative to the (i,j,k) axes
1105
in 3D space is specified using a unit quaternion [a,b,c,d], where
1106
a*a+b*b+c*c+d*d=1. The (b,c,d) values are all that is needed, since
1107
we require that a = sqrt(1.0-(b*b+c*c+d*d)) be nonnegative. The (b,c,d)
1108
values are stored in the (quatern_b,quatern_c,quatern_d) fields.
1109
1110
The quaternion representation is chosen for its compactness in
1111
representing rotations. The (proper) 3x3 rotation matrix that
1112
corresponds to [a,b,c,d] is
1113
1114
[ a*a+b*b-c*c-d*d 2*b*c-2*a*d 2*b*d+2*a*c ]
1115
R = [ 2*b*c+2*a*d a*a+c*c-b*b-d*d 2*c*d-2*a*b ]
1116
[ 2*b*d-2*a*c 2*c*d+2*a*b a*a+d*d-c*c-b*b ]
1117
1118
[ R11 R12 R13 ]
1119
= [ R21 R22 R23 ]
1120
[ R31 R32 R33 ]
1121
1122
If (p,q,r) is a unit 3-vector, then rotation of angle h about that
1123
direction is represented by the quaternion
1124
1125
[a,b,c,d] = [cos(h/2), p*sin(h/2), q*sin(h/2), r*sin(h/2)].
1126
1127
Requiring a >= 0 is equivalent to requiring -Pi <= h <= Pi. (Note that
1128
[-a,-b,-c,-d] represents the same rotation as [a,b,c,d]; there are 2
1129
quaternions that can be used to represent a given rotation matrix R.)
1130
To rotate a 3-vector (x,y,z) using quaternions, we compute the
1131
quaternion product
1132
1133
[0,x',y',z'] = [a,b,c,d] * [0,x,y,z] * [a,-b,-c,-d]
1134
1135
which is equivalent to the matrix-vector multiply
1136
1137
[ x' ] [ x ]
1138
[ y' ] = R [ y ] (equivalence depends on a*a+b*b+c*c+d*d=1)
1139
[ z' ] [ z ]
1140
1141
Multiplication of 2 quaternions is defined by the following:
1142
1143
[a,b,c,d] = a*1 + b*I + c*J + d*K
1144
where
1145
I*I = J*J = K*K = -1 (I,J,K are square roots of -1)
1146
I*J = K J*K = I K*I = J
1147
J*I = -K K*J = -I I*K = -J (not commutative!)
1148
For example
1149
[a,b,0,0] * [0,0,0,1] = [0,0,-b,a]
1150
since this expands to
1151
(a+b*I)*(K) = (a*K+b*I*K) = (a*K-b*J).
1152
1153
The above formula shows how to go from quaternion (b,c,d) to
1154
rotation matrix and direction cosines. Conversely, given R,
1155
we can compute the fields for the NIFTI-1 header by
1156
1157
a = 0.5 * sqrt(1+R11+R22+R33) (not stored)
1158
b = 0.25 * (R32-R23) / a => quatern_b
1159
c = 0.25 * (R13-R31) / a => quatern_c
1160
d = 0.25 * (R21-R12) / a => quatern_d
1161
1162
If a=0 (a 180 degree rotation), alternative formulas are needed.
1163
See the nifti1_io.c function mat44_to_quatern() for an implementation
1164
of the various cases in converting R to [a,b,c,d].
1165
1166
Note that R-transpose (= R-inverse) would lead to the quaternion
1167
[a,-b,-c,-d].
1168
1169
The choice to specify the qoffset_x (etc.) values in the final
1170
coordinate system is partly to make it easy to convert DICOM images to
1171
this format. The DICOM attribute "Image Position (Patient)" (0020,0032)
1172
stores the (Xd,Yd,Zd) coordinates of the center of the first voxel.
1173
Here, (Xd,Yd,Zd) refer to DICOM coordinates, and Xd=-x, Yd=-y, Zd=z,
1174
where (x,y,z) refers to the NIFTI coordinate system discussed above.
1175
(i.e., DICOM +Xd is Left, +Yd is Posterior, +Zd is Superior,
1176
whereas +x is Right, +y is Anterior , +z is Superior. )
1177
Thus, if the (0020,0032) DICOM attribute is extracted into (px,py,pz), then
1178
qoffset_x = -px qoffset_y = -py qoffset_z = pz
1179
is a reasonable setting when qform_code=NIFTI_XFORM_SCANNER_ANAT.
1180
1181
That is, DICOM's coordinate system is 180 degrees rotated about the z-axis
1182
from the neuroscience/NIFTI coordinate system. To transform between DICOM
1183
and NIFTI, you just have to negate the x- and y-coordinates.
1184
1185
The DICOM attribute (0020,0037) "Image Orientation (Patient)" gives the
1186
orientation of the x- and y-axes of the image data in terms of 2 3-vectors.
1187
The first vector is a unit vector along the x-axis, and the second is
1188
along the y-axis. If the (0020,0037) attribute is extracted into the
1189
value (xa,xb,xc,ya,yb,yc), then the first two columns of the R matrix
1190
would be
1191
[ -xa -ya ]
1192
[ -xb -yb ]
1193
[ xc yc ]
1194
The negations are because DICOM's x- and y-axes are reversed relative
1195
to NIFTI's. The third column of the R matrix gives the direction of
1196
displacement (relative to the subject) along the slice-wise direction.
1197
This orientation is not encoded in the DICOM standard in a simple way;
1198
DICOM is mostly concerned with 2D images. The third column of R will be
1199
either the cross-product of the first 2 columns or its negative. It is
1200
possible to infer the sign of the 3rd column by examining the coordinates
1201
in DICOM attribute (0020,0032) "Image Position (Patient)" for successive
1202
slices. However, this method occasionally fails for reasons that I
1203
(RW Cox) do not understand.
1204
-----------------------------------------------------------------------------*/
1205
1206
/* [qs]form_code value: */
/* x,y,z coordinate system refers to: */
1207
/*-----------------------*/
/*---------------------------------------*/
1208
1215
#define NIFTI_XFORM_UNKNOWN 0
1216
1219
#define NIFTI_XFORM_SCANNER_ANAT 1
1220
1224
#define NIFTI_XFORM_ALIGNED_ANAT 2
1225
1229
#define NIFTI_XFORM_TALAIRACH 3
1230
1233
#define NIFTI_XFORM_MNI_152 4
1234
/* @} */
1235
1236
/*---------------------------------------------------------------------------*/
1237
/* UNITS OF SPATIAL AND TEMPORAL DIMENSIONS:
1238
----------------------------------------
1239
The codes below can be used in xyzt_units to indicate the units of pixdim.
1240
As noted earlier, dimensions 1,2,3 are for x,y,z; dimension 4 is for
1241
time (t).
1242
- If dim[4]=1 or dim[0] < 4, there is no time axis.
1243
- A single time series (no space) would be specified with
1244
- dim[0] = 4 (for scalar data) or dim[0] = 5 (for vector data)
1245
- dim[1] = dim[2] = dim[3] = 1
1246
- dim[4] = number of time points
1247
- pixdim[4] = time step
1248
- xyzt_units indicates units of pixdim[4]
1249
- dim[5] = number of values stored at each time point
1250
1251
Bits 0..2 of xyzt_units specify the units of pixdim[1..3]
1252
(e.g., spatial units are values 1..7).
1253
Bits 3..5 of xyzt_units specify the units of pixdim[4]
1254
(e.g., temporal units are multiples of 8).
1255
1256
This compression of 2 distinct concepts into 1 byte is due to the
1257
limited space available in the 348 byte ANALYZE 7.5 header. The
1258
macros XYZT_TO_SPACE and XYZT_TO_TIME can be used to mask off the
1259
undesired bits from the xyzt_units fields, leaving "pure" space
1260
and time codes. Inversely, the macro SPACE_TIME_TO_XYZT can be
1261
used to assemble a space code (0,1,2,...,7) with a time code
1262
(0,8,16,32,...,56) into the combined value for xyzt_units.
1263
1264
Note that codes are provided to indicate the "time" axis units are
1265
actually frequency in Hertz (_HZ), in part-per-million (_PPM)
1266
or in radians-per-second (_RADS).
1267
1268
The toffset field can be used to indicate a nonzero start point for
1269
the time axis. That is, time point #m is at t=toffset+m*pixdim[4]
1270
for m=0..dim[4]-1.
1271
-----------------------------------------------------------------------------*/
1272
1279
#define NIFTI_UNITS_UNKNOWN 0
1280
1283
#define NIFTI_UNITS_METER 1
1284
1285
#define NIFTI_UNITS_MM 2
1286
1287
#define NIFTI_UNITS_MICRON 3
1288
1291
#define NIFTI_UNITS_SEC 8
1292
1293
#define NIFTI_UNITS_MSEC 16
1294
1295
#define NIFTI_UNITS_USEC 24
1296
1297
/*** These units are for spectral data: ***/
1299
#define NIFTI_UNITS_HZ 32
1300
1301
#define NIFTI_UNITS_PPM 40
1302
1303
#define NIFTI_UNITS_RADS 48
1304
/* @} */
1305
1306
#undef XYZT_TO_SPACE
1307
#undef XYZT_TO_TIME
1308
#define XYZT_TO_SPACE(xyzt) ( (xyzt) & 0x07 )
1309
#define XYZT_TO_TIME(xyzt) ( (xyzt) & 0x38 )
1310
1311
#undef SPACE_TIME_TO_XYZT
1312
#define SPACE_TIME_TO_XYZT(ss,tt) ( (((char)(ss)) & 0x07) \
1313
| (((char)(tt)) & 0x38) )
1314
1315
/*---------------------------------------------------------------------------*/
1316
/* MRI-SPECIFIC SPATIAL AND TEMPORAL INFORMATION:
1317
---------------------------------------------
1318
A few fields are provided to store some extra information
1319
that is sometimes important when storing the image data
1320
from an FMRI time series experiment. (After processing such
1321
data into statistical images, these fields are not likely
1322
to be useful.)
1323
1324
{ freq_dim } = These fields encode which spatial dimension (1,2, or 3)
1325
{ phase_dim } = corresponds to which acquisition dimension for MRI data.
1326
{ slice_dim } =
1327
Examples:
1328
Rectangular scan multi-slice EPI:
1329
freq_dim = 1 phase_dim = 2 slice_dim = 3 (or some permutation)
1330
Spiral scan multi-slice EPI:
1331
freq_dim = phase_dim = 0 slice_dim = 3
1332
since the concepts of frequency- and phase-encoding directions
1333
don't apply to spiral scan
1334
1335
slice_duration = If this is positive, AND if slice_dim is nonzero,
1336
indicates the amount of time used to acquire 1 slice.
1337
slice_duration*dim[slice_dim] can be less than pixdim[4]
1338
with a clustered acquisition method, for example.
1339
1340
slice_code = If this is nonzero, AND if slice_dim is nonzero, AND
1341
if slice_duration is positive, indicates the timing
1342
pattern of the slice acquisition. The following codes
1343
are defined:
1344
NIFTI_SLICE_SEQ_INC == sequential increasing
1345
NIFTI_SLICE_SEQ_DEC == sequential decreasing
1346
NIFTI_SLICE_ALT_INC == alternating increasing
1347
NIFTI_SLICE_ALT_DEC == alternating decreasing
1348
NIFTI_SLICE_ALT_INC2 == alternating increasing #2
1349
NIFTI_SLICE_ALT_DEC2 == alternating decreasing #2
1350
{ slice_start } = Indicates the start and end of the slice acquisition
1351
{ slice_end } = pattern, when slice_code is nonzero. These values
1352
are present to allow for the possible addition of
1353
"padded" slices at either end of the volume, which
1354
don't fit into the slice timing pattern. If there
1355
are no padding slices, then slice_start=0 and
1356
slice_end=dim[slice_dim]-1 are the correct values.
1357
For these values to be meaningful, slice_start must
1358
be non-negative and slice_end must be greater than
1359
slice_start. Otherwise, they should be ignored.
1360
1361
The following table indicates the slice timing pattern, relative to
1362
time=0 for the first slice acquired, for some sample cases. Here,
1363
dim[slice_dim]=7 (there are 7 slices, labeled 0..6), slice_duration=0.1,
1364
and slice_start=1, slice_end=5 (1 padded slice on each end).
1365
1366
slice
1367
index SEQ_INC SEQ_DEC ALT_INC ALT_DEC ALT_INC2 ALT_DEC2
1368
6 : n/a n/a n/a n/a n/a n/a n/a = not applicable
1369
5 : 0.4 0.0 0.2 0.0 0.4 0.2 (slice time offset
1370
4 : 0.3 0.1 0.4 0.3 0.1 0.0 doesn't apply to
1371
3 : 0.2 0.2 0.1 0.1 0.3 0.3 slices outside
1372
2 : 0.1 0.3 0.3 0.4 0.0 0.1 the range
1373
1 : 0.0 0.4 0.0 0.2 0.2 0.4 slice_start ..
1374
0 : n/a n/a n/a n/a n/a n/a slice_end)
1375
1376
The SEQ slice_codes are sequential ordering (uncommon but not unknown),
1377
either increasing in slice number or decreasing (INC or DEC), as
1378
illustrated above.
1379
1380
The ALT slice codes are alternating ordering. The 'standard' way for
1381
these to operate (without the '2' on the end) is for the slice timing
1382
to start at the edge of the slice_start .. slice_end group (at slice_start
1383
for INC and at slice_end for DEC). For the 'ALT_*2' slice_codes, the
1384
slice timing instead starts at the first slice in from the edge (at
1385
slice_start+1 for INC2 and at slice_end-1 for DEC2). This latter
1386
acquisition scheme is found on some Siemens scanners.
1387
1388
The fields freq_dim, phase_dim, slice_dim are all squished into the single
1389
byte field dim_info (2 bits each, since the values for each field are
1390
limited to the range 0..3). This unpleasantness is due to lack of space
1391
in the 348 byte allowance.
1392
1393
The macros DIM_INFO_TO_FREQ_DIM, DIM_INFO_TO_PHASE_DIM, and
1394
DIM_INFO_TO_SLICE_DIM can be used to extract these values from the
1395
dim_info byte.
1396
1397
The macro FPS_INTO_DIM_INFO can be used to put these 3 values
1398
into the dim_info byte.
1399
-----------------------------------------------------------------------------*/
1400
1401
#undef DIM_INFO_TO_FREQ_DIM
1402
#undef DIM_INFO_TO_PHASE_DIM
1403
#undef DIM_INFO_TO_SLICE_DIM
1404
1405
#define DIM_INFO_TO_FREQ_DIM(di) ( ((di) ) & 0x03 )
1406
#define DIM_INFO_TO_PHASE_DIM(di) ( ((di) >> 2) & 0x03 )
1407
#define DIM_INFO_TO_SLICE_DIM(di) ( ((di) >> 4) & 0x03 )
1408
1409
#undef FPS_INTO_DIM_INFO
1410
#define FPS_INTO_DIM_INFO(fd,pd,sd) ( ( ( ((char)(fd)) & 0x03) ) | \
1411
( ( ((char)(pd)) & 0x03) << 2 ) | \
1412
( ( ((char)(sd)) & 0x03) << 4 ) )
1413
1419
#define NIFTI_SLICE_UNKNOWN 0
1420
#define NIFTI_SLICE_SEQ_INC 1
1421
#define NIFTI_SLICE_SEQ_DEC 2
1422
#define NIFTI_SLICE_ALT_INC 3
1423
#define NIFTI_SLICE_ALT_DEC 4
1424
#define NIFTI_SLICE_ALT_INC2 5
/* 05 May 2005: RWCox */
1425
#define NIFTI_SLICE_ALT_DEC2 6
/* 05 May 2005: RWCox */
1426
/* @} */
1427
1428
/*---------------------------------------------------------------------------*/
1429
/* UNUSED FIELDS:
1430
-------------
1431
Some of the ANALYZE 7.5 fields marked as ++UNUSED++ may need to be set
1432
to particular values for compatibility with other programs. The issue
1433
of interoperability of ANALYZE 7.5 files is a murky one -- not all
1434
programs require exactly the same set of fields. (Unobscuring this
1435
murkiness is a principal motivation behind NIFTI-1.)
1436
1437
Some of the fields that may need to be set for other (non-NIFTI aware)
1438
software to be happy are:
1439
1440
extents dbh.h says this should be 16384
1441
regular dbh.h says this should be the character 'r'
1442
glmin, } dbh.h says these values should be the min and max voxel
1443
glmax } values for the entire dataset
1444
1445
It is best to initialize ALL fields in the NIFTI-1 header to 0
1446
(e.g., with calloc()), then fill in what is needed.
1447
-----------------------------------------------------------------------------*/
1448
1449
/*---------------------------------------------------------------------------*/
1450
/* MISCELLANEOUS C MACROS
1451
-----------------------------------------------------------------------------*/
1452
1453
/*.................*/
1457
#define NIFTI_VERSION(h) \
1458
( ( (h).magic[0]=='n' && (h).magic[3]=='\0' && \
1459
( (h).magic[1]=='i' || (h).magic[1]=='+' ) && \
1460
( (h).magic[2]>='1' && (h).magic[2]<='9' ) ) \
1461
? (h).magic[2]-'0' : 0 )
1462
1463
/*.................*/
1468
#define NIFTI_ONEFILE(h) ( (h).magic[1] == '+' )
1469
1470
/*.................*/
1474
#define NIFTI_NEEDS_SWAP(h) ( (h).dim[0] < 0 || (h).dim[0] > 7 )
1475
1476
/*.................*/
1480
#define NIFTI_5TH_DIM(h) ( ((h).dim[0]>4 && (h).dim[5]>1) ? (h).dim[5] : 0 )
1481
1482
/*****************************************************************************/
1483
1484
/*=================*/
1485
#ifdef __cplusplus
1486
}
1487
#endif
1488
/*=================*/
1489
1490
#endif
/* _NIFTI_HEADER_ */
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