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nifti1.h
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1
16#ifndef _NIFTI_HEADER_
17#define _NIFTI_HEADER_
18
19/*****************************************************************************
20 ** This file defines the "NIFTI-1" header format. **
21 ** It is derived from 2 meetings at the NIH (31 Mar 2003 and **
22 ** 02 Sep 2003) of the Data Format Working Group (DFWG), **
23 ** chartered by the NIfTI (Neuroimaging Informatics Technology **
24 ** Initiative) at the National Institutes of Health (NIH). **
25 **--------------------------------------------------------------**
26 ** Neither the National Institutes of Health (NIH), the DFWG, **
27 ** nor any of the members or employees of these institutions **
28 ** imply any warranty of usefulness of this material for any **
29 ** purpose, and do not assume any liability for damages, **
30 ** incidental or otherwise, caused by any use of this document. **
31 ** If these conditions are not acceptable, do not use this! **
32 **--------------------------------------------------------------**
33 ** Author: Robert W Cox (NIMH, Bethesda) **
34 ** Advisors: John Ashburner (FIL, London), **
35 ** Stephen Smith (FMRIB, Oxford), **
36 ** Mark Jenkinson (FMRIB, Oxford) **
37******************************************************************************/
38
39/*---------------------------------------------------------------------------*/
40/* Note that the ANALYZE 7.5 file header (dbh.h) is
41 (c) Copyright 1986-1995
42 Biomedical Imaging Resource
43 Mayo Foundation
44 Incorporation of components of dbh.h are by permission of the
45 Mayo Foundation.
46
47 Changes from the ANALYZE 7.5 file header in this file are released to the
48 public domain, including the functional comments and any amusing asides.
49-----------------------------------------------------------------------------*/
50
51/*---------------------------------------------------------------------------*/
119/*---------------------------------------------------------------------------*/
120/* HEADER STRUCT DECLARATION:
121 -------------------------
122 In the comments below for each field, only NIFTI-1 specific requirements
123 or changes from the ANALYZE 7.5 format are described. For convenience,
124 the 348 byte header is described as a single struct, rather than as the
125 ANALYZE 7.5 group of 3 substructs.
126
127 Further comments about the interpretation of various elements of this
128 header are after the data type definition itself. Fields that are
129 marked as ++UNUSED++ have no particular interpretation in this standard.
130 (Also see the UNUSED FIELDS comment section, far below.)
131
132 The presumption below is that the various C types have particular sizes:
133 sizeof(int) = sizeof(float) = 4 ; sizeof(short) = 2
134-----------------------------------------------------------------------------*/
135
136/*=================*/
137#ifdef __cplusplus
138extern "C" {
139#endif
140/*=================*/
141
147 /*************************/ /************************/
148struct nifti_1_header { /* NIFTI-1 usage */ /* ANALYZE 7.5 field(s) */
149 /*************************/ /************************/
150
151 /*--- was header_key substruct ---*/
152 int sizeof_hdr; /* int sizeof_hdr; */
153 char data_type[10]; /* char data_type[10]; */
154 char db_name[18]; /* char db_name[18]; */
155 int extents; /* int extents; */
156 short session_error; /* short session_error; */
157 char regular; /* char regular; */
158 char dim_info; /* char hkey_un0; */
159
160 /*--- was image_dimension substruct ---*/
161 short dim[8]; /* short dim[8]; */
162 float intent_p1 ; /* short unused8; */
163 /* short unused9; */
164 float intent_p2 ; /* short unused10; */
165 /* short unused11; */
166 float intent_p3 ; /* short unused12; */
167 /* short unused13; */
168 short intent_code ; /* short unused14; */
169 short datatype; /* short datatype; */
170 short bitpix; /* short bitpix; */
171 short slice_start; /* short dim_un0; */
172 float pixdim[8]; /* float pixdim[8]; */
173 float vox_offset; /* float vox_offset; */
174 float scl_slope ; /* float funused1; */
175 float scl_inter ; /* float funused2; */
176 short slice_end; /* float funused3; */
179 float cal_max; /* float cal_max; */
180 float cal_min; /* float cal_min; */
181 float slice_duration; /* float compressed; */
182 float toffset; /* float verified; */
183 int glmax; /* int glmax; */
184 int glmin; /* int glmin; */
185
186 /*--- was data_history substruct ---*/
187 char descrip[80]; /* char descrip[80]; */
188 char aux_file[24]; /* char aux_file[24]; */
189
190 short qform_code ; /*-- all ANALYZE 7.5 ---*/
191 short sform_code ; /* fields below here */
192 /* are replaced */
193 float quatern_b ;
194 float quatern_c ;
195 float quatern_d ;
196 float qoffset_x ;
197 float qoffset_y ;
198 float qoffset_z ;
200 float srow_x[4] ;
201 float srow_y[4] ;
202 float srow_z[4] ;
204 char intent_name[16];
206 char magic[4] ;
208} ; /**** 348 bytes total ****/
209
210typedef struct nifti_1_header nifti_1_header ;
211
212/*---------------------------------------------------------------------------*/
213/* HEADER EXTENSIONS:
214 -----------------
215 After the end of the 348 byte header (e.g., after the magic field),
216 the next 4 bytes are a char array field named "extension". By default,
217 all 4 bytes of this array should be set to zero. In a .nii file, these
218 4 bytes will always be present, since the earliest start point for
219 the image data is byte #352. In a separate .hdr file, these bytes may
220 or may not be present. If not present (i.e., if the length of the .hdr
221 file is 348 bytes), then a NIfTI-1 compliant program should use the
222 default value of extension={0,0,0,0}. The first byte (extension[0])
223 is the only value of this array that is specified at present. The other
224 3 bytes are reserved for future use.
225
226 If extension[0] is nonzero, it indicates that extended header information
227 is present in the bytes following the extension array. In a .nii file,
228 this extended header data is before the image data (and vox_offset
229 must be set correctly to allow for this). In a .hdr file, this extended
230 data follows extension and proceeds (potentially) to the end of the file.
231
232 The format of extended header data is weakly specified. Each extension
233 must be an integer multiple of 16 bytes long. The first 8 bytes of each
234 extension comprise 2 integers:
235 int esize , ecode ;
236 These values may need to be byte-swapped, as indicated by dim[0] for
237 the rest of the header.
238 * esize is the number of bytes that form the extended header data
239 + esize must be a positive integral multiple of 16
240 + this length includes the 8 bytes of esize and ecode themselves
241 * ecode is a non-negative integer that indicates the format of the
242 extended header data that follows
243 + different ecode values are assigned to different developer groups
244 + at present, the "registered" values for code are
245 = 0 = unknown private format (not recommended!)
246 = 2 = DICOM format (i.e., attribute tags and values)
247 = 4 = AFNI group (i.e., ASCII XML-ish elements)
248 In the interests of interoperability (a primary rationale for NIfTI),
249 groups developing software that uses this extension mechanism are
250 encouraged to document and publicize the format of their extensions.
251 To this end, the NIfTI DFWG will assign even numbered codes upon request
252 to groups submitting at least rudimentary documentation for the format
253 of their extension; at present, the contact is mailto:rwcox@nih.gov.
254 The assigned codes and documentation will be posted on the NIfTI
255 website. All odd values of ecode (and 0) will remain unassigned;
256 at least, until the even ones are used up, when we get to 2,147,483,646.
257
258 Note that the other contents of the extended header data section are
259 totally unspecified by the NIfTI-1 standard. In particular, if binary
260 data is stored in such a section, its byte order is not necessarily
261 the same as that given by examining dim[0]; it is incumbent on the
262 programs dealing with such data to determine the byte order of binary
263 extended header data.
264
265 Multiple extended header sections are allowed, each starting with an
266 esize,ecode value pair. The first esize value, as described above,
267 is at bytes #352-355 in the .hdr or .nii file (files start at byte #0).
268 If this value is positive, then the second (esize2) will be found
269 starting at byte #352+esize1 , the third (esize3) at byte #352+esize1+esize2,
270 et cetera. Of course, in a .nii file, the value of vox_offset must
271 be compatible with these extensions. If a malformed file indicates
272 that an extended header data section would run past vox_offset, then
273 the entire extended header section should be ignored. In a .hdr file,
274 if an extended header data section would run past the end-of-file,
275 that extended header data should also be ignored.
276
277 With the above scheme, a program can successively examine the esize
278 and ecode values, and skip over each extended header section if the
279 program doesn't know how to interpret the data within. Of course, any
280 program can simply ignore all extended header sections simply by jumping
281 straight to the image data using vox_offset.
282-----------------------------------------------------------------------------*/
283
291struct nifti1_extender { char extension[4] ; } ;
292typedef struct nifti1_extender nifti1_extender ;
293
298 int esize ;
299 int ecode ;
300 char * edata ;
301} ;
302typedef struct nifti1_extension nifti1_extension ;
303
304/*---------------------------------------------------------------------------*/
305/* DATA DIMENSIONALITY (as in ANALYZE 7.5):
306 ---------------------------------------
307 dim[0] = number of dimensions;
308 - if dim[0] is outside range 1..7, then the header information
309 needs to be byte swapped appropriately
310 - ANALYZE supports dim[0] up to 7, but NIFTI-1 reserves
311 dimensions 1,2,3 for space (x,y,z), 4 for time (t), and
312 5,6,7 for anything else needed.
313
314 dim[i] = length of dimension #i, for i=1..dim[0] (must be positive)
315 - also see the discussion of intent_code, far below
316
317 pixdim[i] = voxel width along dimension #i, i=1..dim[0] (positive)
318 - cf. ORIENTATION section below for use of pixdim[0]
319 - the units of pixdim can be specified with the xyzt_units
320 field (also described far below).
321
322 Number of bits per voxel value is in bitpix, which MUST correspond with
323 the datatype field. The total number of bytes in the image data is
324 dim[1] * ... * dim[dim[0]] * bitpix / 8
325
326 In NIFTI-1 files, dimensions 1,2,3 are for space, dimension 4 is for time,
327 and dimension 5 is for storing multiple values at each spatiotemporal
328 voxel. Some examples:
329 - A typical whole-brain FMRI experiment's time series:
330 - dim[0] = 4
331 - dim[1] = 64 pixdim[1] = 3.75 xyzt_units = NIFTI_UNITS_MM
332 - dim[2] = 64 pixdim[2] = 3.75 | NIFTI_UNITS_SEC
333 - dim[3] = 20 pixdim[3] = 5.0
334 - dim[4] = 120 pixdim[4] = 2.0
335 - A typical T1-weighted anatomical volume:
336 - dim[0] = 3
337 - dim[1] = 256 pixdim[1] = 1.0 xyzt_units = NIFTI_UNITS_MM
338 - dim[2] = 256 pixdim[2] = 1.0
339 - dim[3] = 128 pixdim[3] = 1.1
340 - A single slice EPI time series:
341 - dim[0] = 4
342 - dim[1] = 64 pixdim[1] = 3.75 xyzt_units = NIFTI_UNITS_MM
343 - dim[2] = 64 pixdim[2] = 3.75 | NIFTI_UNITS_SEC
344 - dim[3] = 1 pixdim[3] = 5.0
345 - dim[4] = 1200 pixdim[4] = 0.2
346 - A 3-vector stored at each point in a 3D volume:
347 - dim[0] = 5
348 - dim[1] = 256 pixdim[1] = 1.0 xyzt_units = NIFTI_UNITS_MM
349 - dim[2] = 256 pixdim[2] = 1.0
350 - dim[3] = 128 pixdim[3] = 1.1
351 - dim[4] = 1 pixdim[4] = 0.0
352 - dim[5] = 3 intent_code = NIFTI_INTENT_VECTOR
353 - A single time series with a 3x3 matrix at each point:
354 - dim[0] = 5
355 - dim[1] = 1 xyzt_units = NIFTI_UNITS_SEC
356 - dim[2] = 1
357 - dim[3] = 1
358 - dim[4] = 1200 pixdim[4] = 0.2
359 - dim[5] = 9 intent_code = NIFTI_INTENT_GENMATRIX
360 - intent_p1 = intent_p2 = 3.0 (indicates matrix dimensions)
361-----------------------------------------------------------------------------*/
362
363/*---------------------------------------------------------------------------*/
364/* DATA STORAGE:
365 ------------
366 If the magic field is "n+1", then the voxel data is stored in the
367 same file as the header. In this case, the voxel data starts at offset
368 (int)vox_offset into the header file. Thus, vox_offset=352.0 means that
369 the data starts immediately after the NIFTI-1 header. If vox_offset is
370 greater than 352, the NIFTI-1 format does not say much about the
371 contents of the dataset file between the end of the header and the
372 start of the data.
373
374 FILES:
375 -----
376 If the magic field is "ni1", then the voxel data is stored in the
377 associated ".img" file, starting at offset 0 (i.e., vox_offset is not
378 used in this case, and should be set to 0.0).
379
380 When storing NIFTI-1 datasets in pairs of files, it is customary to name
381 the files in the pattern "name.hdr" and "name.img", as in ANALYZE 7.5.
382 When storing in a single file ("n+1"), the file name should be in
383 the form "name.nii" (the ".nft" and ".nif" suffixes are already taken;
384 cf. http://www.icdatamaster.com/n.html ).
385
386 BYTE ORDERING:
387 -------------
388 The byte order of the data arrays is presumed to be the same as the byte
389 order of the header (which is determined by examining dim[0]).
390
391 Floating point types are presumed to be stored in IEEE-754 format.
392-----------------------------------------------------------------------------*/
393
394/*---------------------------------------------------------------------------*/
395/* DETAILS ABOUT vox_offset:
396 ------------------------
397 In a .nii file, the vox_offset field value is interpreted as the start
398 location of the image data bytes in that file. In a .hdr/.img file pair,
399 the vox_offset field value is the start location of the image data
400 bytes in the .img file.
401 * If vox_offset is less than 352 in a .nii file, it is equivalent
402 to 352 (i.e., image data never starts before byte #352 in a .nii file).
403 * The default value for vox_offset in a .nii file is 352.
404 * In a .hdr file, the default value for vox_offset is 0.
405 * vox_offset should be an integer multiple of 16; otherwise, some
406 programs may not work properly (e.g., SPM). This is to allow
407 memory-mapped input to be properly byte-aligned.
408 Note that since vox_offset is an IEEE-754 32 bit float (for compatibility
409 with the ANALYZE-7.5 format), it effectively has a 24 bit mantissa. All
410 integers from 0 to 2^24 can be represented exactly in this format, but not
411 all larger integers are exactly storable as IEEE-754 32 bit floats. However,
412 unless you plan to have vox_offset be potentially larger than 16 MB, this
413 should not be an issue. (Actually, any integral multiple of 16 up to 2^27
414 can be represented exactly in this format, which allows for up to 128 MB
415 of random information before the image data. If that isn't enough, then
416 perhaps this format isn't right for you.)
417
418 In a .img file (i.e., image data stored separately from the NIfTI-1
419 header), data bytes between #0 and #vox_offset-1 (inclusive) are completely
420 undefined and unregulated by the NIfTI-1 standard. One potential use of
421 having vox_offset > 0 in the .hdr/.img file pair storage method is to make
422 the .img file be a copy of (or link to) a pre-existing image file in some
423 other format, such as DICOM; then vox_offset would be set to the offset of
424 the image data in this file. (It may not be possible to follow the
425 "multiple-of-16 rule" with an arbitrary external file; using the NIfTI-1
426 format in such a case may lead to a file that is incompatible with software
427 that relies on vox_offset being a multiple of 16.)
428
429 In a .nii file, data bytes between #348 and #vox_offset-1 (inclusive) may
430 be used to store user-defined extra information; similarly, in a .hdr file,
431 any data bytes after byte #347 are available for user-defined extra
432 information. The (very weak) regulation of this extra header data is
433 described elsewhere.
434-----------------------------------------------------------------------------*/
435
436/*---------------------------------------------------------------------------*/
437/* DATA SCALING:
438 ------------
439 If the scl_slope field is nonzero, then each voxel value in the dataset
440 should be scaled as
441 y = scl_slope * x + scl_inter
442 where x = voxel value stored
443 y = "true" voxel value
444 Normally, we would expect this scaling to be used to store "true" floating
445 values in a smaller integer datatype, but that is not required. That is,
446 it is legal to use scaling even if the datatype is a float type (crazy,
447 perhaps, but legal).
448 - However, the scaling is to be ignored if datatype is DT_RGB24.
449 - If datatype is a complex type, then the scaling is to be
450 applied to both the real and imaginary parts.
451
452 The cal_min and cal_max fields (if nonzero) are used for mapping (possibly
453 scaled) dataset values to display colors:
454 - Minimum display intensity (black) corresponds to dataset value cal_min.
455 - Maximum display intensity (white) corresponds to dataset value cal_max.
456 - Dataset values below cal_min should display as black also, and values
457 above cal_max as white.
458 - Colors "black" and "white", of course, may refer to any scalar display
459 scheme (e.g., a color lookup table specified via aux_file).
460 - cal_min and cal_max only make sense when applied to scalar-valued
461 datasets (i.e., dim[0] < 5 or dim[5] = 1).
462-----------------------------------------------------------------------------*/
463
464/*---------------------------------------------------------------------------*/
465/* TYPE OF DATA (acceptable values for datatype field):
466 ---------------------------------------------------
467 Values of datatype smaller than 256 are ANALYZE 7.5 compatible.
468 Larger values are NIFTI-1 additions. These are all multiples of 256, so
469 that no bits below position 8 are set in datatype. But there is no need
470 to use only powers-of-2, as the original ANALYZE 7.5 datatype codes do.
471
472 The additional codes are intended to include a complete list of basic
473 scalar types, including signed and unsigned integers from 8 to 64 bits,
474 floats from 32 to 128 bits, and complex (float pairs) from 64 to 256 bits.
475
476 Note that most programs will support only a few of these datatypes!
477 A NIFTI-1 program should fail gracefully (e.g., print a warning message)
478 when it encounters a dataset with a type it doesn't like.
479-----------------------------------------------------------------------------*/
480
481#undef DT_UNKNOWN /* defined in dirent.h on some Unix systems */
482
487 /*--- the original ANALYZE 7.5 type codes ---*/
488#define DT_NONE 0
489#define DT_UNKNOWN 0 /* what it says, dude */
490#define DT_BINARY 1 /* binary (1 bit/voxel) */
491#define DT_UNSIGNED_CHAR 2 /* unsigned char (8 bits/voxel) */
492#define DT_SIGNED_SHORT 4 /* signed short (16 bits/voxel) */
493#define DT_SIGNED_INT 8 /* signed int (32 bits/voxel) */
494#define DT_FLOAT 16 /* float (32 bits/voxel) */
495#define DT_COMPLEX 32 /* complex (64 bits/voxel) */
496#define DT_DOUBLE 64 /* double (64 bits/voxel) */
497#define DT_RGB 128 /* RGB triple (24 bits/voxel) */
498#define DT_ALL 255 /* not very useful (?) */
499
500 /*----- another set of names for the same ---*/
501#define DT_UINT8 2
502#define DT_INT16 4
503#define DT_INT32 8
504#define DT_FLOAT32 16
505#define DT_COMPLEX64 32
506#define DT_FLOAT64 64
507#define DT_RGB24 128
508
509 /*------------------- new codes for NIFTI ---*/
510#define DT_INT8 256 /* signed char (8 bits) */
511#define DT_UINT16 512 /* unsigned short (16 bits) */
512#define DT_UINT32 768 /* unsigned int (32 bits) */
513#define DT_INT64 1024 /* long long (64 bits) */
514#define DT_UINT64 1280 /* unsigned long long (64 bits) */
515#define DT_FLOAT128 1536 /* long double (128 bits) */
516#define DT_COMPLEX128 1792 /* double pair (128 bits) */
517#define DT_COMPLEX256 2048 /* long double pair (256 bits) */
518#define DT_RGBA32 2304 /* 4 byte RGBA (32 bits/voxel) */
519/* @} */
520
521
522 /*------- aliases for all the above codes ---*/
523
529#define NIFTI_TYPE_UINT8 2
531#define NIFTI_TYPE_INT16 4
533#define NIFTI_TYPE_INT32 8
535#define NIFTI_TYPE_FLOAT32 16
537#define NIFTI_TYPE_COMPLEX64 32
539#define NIFTI_TYPE_FLOAT64 64
541#define NIFTI_TYPE_RGB24 128
543#define NIFTI_TYPE_INT8 256
545#define NIFTI_TYPE_UINT16 512
547#define NIFTI_TYPE_UINT32 768
549#define NIFTI_TYPE_INT64 1024
551#define NIFTI_TYPE_UINT64 1280
553#define NIFTI_TYPE_FLOAT128 1536
555#define NIFTI_TYPE_COMPLEX128 1792
557#define NIFTI_TYPE_COMPLEX256 2048
559#define NIFTI_TYPE_RGBA32 2304
560/* @} */
561
562 /*-------- sample typedefs for complicated types ---*/
563#if 0
564typedef struct { float r,i; } complex_float ;
565typedef struct { double r,i; } complex_double ;
566typedef struct { long double r,i; } complex_longdouble ;
567typedef struct { unsigned char r,g,b; } rgb_byte ;
568#endif
569
570/*---------------------------------------------------------------------------*/
571/* INTERPRETATION OF VOXEL DATA:
572 ----------------------------
573 The intent_code field can be used to indicate that the voxel data has
574 some particular meaning. In particular, a large number of codes is
575 given to indicate that the the voxel data should be interpreted as
576 being drawn from a given probability distribution.
577
578 VECTOR-VALUED DATASETS:
579 ----------------------
580 The 5th dimension of the dataset, if present (i.e., dim[0]=5 and
581 dim[5] > 1), contains multiple values (e.g., a vector) to be stored
582 at each spatiotemporal location. For example, the header values
583 - dim[0] = 5
584 - dim[1] = 64
585 - dim[2] = 64
586 - dim[3] = 20
587 - dim[4] = 1 (indicates no time axis)
588 - dim[5] = 3
589 - datatype = DT_FLOAT
590 - intent_code = NIFTI_INTENT_VECTOR
591 mean that this dataset should be interpreted as a 3D volume (64x64x20),
592 with a 3-vector of floats defined at each point in the 3D grid.
593
594 A program reading a dataset with a 5th dimension may want to reformat
595 the image data to store each voxels' set of values together in a struct
596 or array. This programming detail, however, is beyond the scope of the
597 NIFTI-1 file specification! Uses of dimensions 6 and 7 are also not
598 specified here.
599
600 STATISTICAL PARAMETRIC DATASETS (i.e., SPMs):
601 --------------------------------------------
602 Values of intent_code from NIFTI_FIRST_STATCODE to NIFTI_LAST_STATCODE
603 (inclusive) indicate that the numbers in the dataset should be interpreted
604 as being drawn from a given distribution. Most such distributions have
605 auxiliary parameters (e.g., NIFTI_INTENT_TTEST has 1 DOF parameter).
606
607 If the dataset DOES NOT have a 5th dimension, then the auxiliary parameters
608 are the same for each voxel, and are given in header fields intent_p1,
609 intent_p2, and intent_p3.
610
611 If the dataset DOES have a 5th dimension, then the auxiliary parameters
612 are different for each voxel. For example, the header values
613 - dim[0] = 5
614 - dim[1] = 128
615 - dim[2] = 128
616 - dim[3] = 1 (indicates a single slice)
617 - dim[4] = 1 (indicates no time axis)
618 - dim[5] = 2
619 - datatype = DT_FLOAT
620 - intent_code = NIFTI_INTENT_TTEST
621 mean that this is a 2D dataset (128x128) of t-statistics, with the
622 t-statistic being in the first "plane" of data and the degrees-of-freedom
623 parameter being in the second "plane" of data.
624
625 If the dataset 5th dimension is used to store the voxel-wise statistical
626 parameters, then dim[5] must be 1 plus the number of parameters required
627 by that distribution (e.g., intent_code=NIFTI_INTENT_TTEST implies dim[5]
628 must be 2, as in the example just above).
629
630 Note: intent_code values 2..10 are compatible with AFNI 1.5x (which is
631 why there is no code with value=1, which is obsolescent in AFNI).
632
633 OTHER INTENTIONS:
634 ----------------
635 The purpose of the intent_* fields is to help interpret the values
636 stored in the dataset. Some non-statistical values for intent_code
637 and conventions are provided for storing other complex data types.
638
639 The intent_name field provides space for a 15 character (plus 0 byte)
640 'name' string for the type of data stored. Examples:
641 - intent_code = NIFTI_INTENT_ESTIMATE; intent_name = "T1";
642 could be used to signify that the voxel values are estimates of the
643 NMR parameter T1.
644 - intent_code = NIFTI_INTENT_TTEST; intent_name = "House";
645 could be used to signify that the voxel values are t-statistics
646 for the significance of 'activation' response to a House stimulus.
647 - intent_code = NIFTI_INTENT_DISPVECT; intent_name = "ToMNI152";
648 could be used to signify that the voxel values are a displacement
649 vector that transforms each voxel (x,y,z) location to the
650 corresponding location in the MNI152 standard brain.
651 - intent_code = NIFTI_INTENT_SYMMATRIX; intent_name = "DTI";
652 could be used to signify that the voxel values comprise a diffusion
653 tensor image.
654
655 If no data name is implied or needed, intent_name[0] should be set to 0.
656-----------------------------------------------------------------------------*/
657
660#define NIFTI_INTENT_NONE 0
661
662 /*-------- These codes are for probability distributions ---------------*/
663 /* Most distributions have a number of parameters,
664 below denoted by p1, p2, and p3, and stored in
665 - intent_p1, intent_p2, intent_p3 if dataset doesn't have 5th dimension
666 - image data array if dataset does have 5th dimension
667
668 Functions to compute with many of the distributions below can be found
669 in the CDF library from U Texas.
670
671 Formulas for and discussions of these distributions can be found in the
672 following books:
673
674 [U] Univariate Discrete Distributions,
675 NL Johnson, S Kotz, AW Kemp.
676
677 [C1] Continuous Univariate Distributions, vol. 1,
678 NL Johnson, S Kotz, N Balakrishnan.
679
680 [C2] Continuous Univariate Distributions, vol. 2,
681 NL Johnson, S Kotz, N Balakrishnan. */
682 /*----------------------------------------------------------------------*/
683
692#define NIFTI_INTENT_CORREL 2
693
696#define NIFTI_INTENT_TTEST 3
697
701#define NIFTI_INTENT_FTEST 4
702
705#define NIFTI_INTENT_ZSCORE 5
706
710#define NIFTI_INTENT_CHISQ 6
711
715#define NIFTI_INTENT_BETA 7
716
721#define NIFTI_INTENT_BINOM 8
722
727#define NIFTI_INTENT_GAMMA 9
728
732#define NIFTI_INTENT_POISSON 10
733
737#define NIFTI_INTENT_NORMAL 11
738
743#define NIFTI_INTENT_FTEST_NONC 12
744
748#define NIFTI_INTENT_CHISQ_NONC 13
749
754#define NIFTI_INTENT_LOGISTIC 14
755
760#define NIFTI_INTENT_LAPLACE 15
761
764#define NIFTI_INTENT_UNIFORM 16
765
769#define NIFTI_INTENT_TTEST_NONC 17
770
776#define NIFTI_INTENT_WEIBULL 18
777
784#define NIFTI_INTENT_CHI 19
785
791#define NIFTI_INTENT_INVGAUSS 20
792
797#define NIFTI_INTENT_EXTVAL 21
798
801#define NIFTI_INTENT_PVAL 22
802
809#define NIFTI_INTENT_LOGPVAL 23
810
816#define NIFTI_INTENT_LOG10PVAL 24
817
820#define NIFTI_FIRST_STATCODE 2
821
824#define NIFTI_LAST_STATCODE 24
825
826 /*---------- these values for intent_code aren't for statistics ----------*/
827
832#define NIFTI_INTENT_ESTIMATE 1001
833
838#define NIFTI_INTENT_LABEL 1002
839
843#define NIFTI_INTENT_NEURONAME 1003
844
857#define NIFTI_INTENT_GENMATRIX 1004
858
870#define NIFTI_INTENT_SYMMATRIX 1005
871
879#define NIFTI_INTENT_DISPVECT 1006 /* specifically for displacements */
880#define NIFTI_INTENT_VECTOR 1007 /* for any other type of vector */
881
893#define NIFTI_INTENT_POINTSET 1008
894
906#define NIFTI_INTENT_TRIANGLE 1009
907
915#define NIFTI_INTENT_QUATERNION 1010
916
920#define NIFTI_INTENT_DIMLESS 1011
921
922 /*---------- these values apply to GIFTI datasets ----------*/
923
926#define NIFTI_INTENT_TIME_SERIES 2001
927
931#define NIFTI_INTENT_NODE_INDEX 2002
932
942#define NIFTI_INTENT_RGB_VECTOR 2003
943
953#define NIFTI_INTENT_RGBA_VECTOR 2004
954
958#define NIFTI_INTENT_SHAPE 2005
959
969#define NIFTI_INTENT_FSL_FNIRT_DISPLACEMENT_FIELD 2006
970#define NIFTI_INTENT_FSL_CUBIC_SPLINE_COEFFICIENTS 2007
971#define NIFTI_INTENT_FSL_DCT_COEFFICIENTS 2008
972#define NIFTI_INTENT_FSL_QUADRATIC_SPLINE_COEFFICIENTS 2009
973
983#define NIFTI_INTENT_FSL_TOPUP_CUBIC_SPLINE_COEFFICIENTS 2016
984#define NIFTI_INTENT_FSL_TOPUP_QUADRATIC_SPLINE_COEFFICIENTS 2017
985#define NIFTI_INTENT_FSL_TOPUP_FIELD 2018
986
987/* @} */
988
989/*---------------------------------------------------------------------------*/
990/* 3D IMAGE (VOLUME) ORIENTATION AND LOCATION IN SPACE:
991 ---------------------------------------------------
992 There are 3 different methods by which continuous coordinates can
993 attached to voxels. The discussion below emphasizes 3D volumes, and
994 the continuous coordinates are referred to as (x,y,z). The voxel
995 index coordinates (i.e., the array indexes) are referred to as (i,j,k),
996 with valid ranges:
997 i = 0 .. dim[1]-1
998 j = 0 .. dim[2]-1 (if dim[0] >= 2)
999 k = 0 .. dim[3]-1 (if dim[0] >= 3)
1000 The (x,y,z) coordinates refer to the CENTER of a voxel. In methods
1001 2 and 3, the (x,y,z) axes refer to a subject-based coordinate system,
1002 with
1003 +x = Right +y = Anterior +z = Superior.
1004 This is a right-handed coordinate system. However, the exact direction
1005 these axes point with respect to the subject depends on qform_code
1006 (Method 2) and sform_code (Method 3).
1007
1008 N.B.: The i index varies most rapidly, j index next, k index slowest.
1009 Thus, voxel (i,j,k) is stored starting at location
1010 (i + j*dim[1] + k*dim[1]*dim[2]) * (bitpix/8)
1011 into the dataset array.
1012
1013 N.B.: The ANALYZE 7.5 coordinate system is
1014 +x = Left +y = Anterior +z = Superior
1015 which is a left-handed coordinate system. This backwardness is
1016 too difficult to tolerate, so this NIFTI-1 standard specifies the
1017 coordinate order which is most common in functional neuroimaging.
1018
1019 N.B.: The 3 methods below all give the locations of the voxel centers
1020 in the (x,y,z) coordinate system. In many cases, programs will wish
1021 to display image data on some other grid. In such a case, the program
1022 will need to convert its desired (x,y,z) values into (i,j,k) values
1023 in order to extract (or interpolate) the image data. This operation
1024 would be done with the inverse transformation to those described below.
1025
1026 N.B.: Method 2 uses a factor 'qfac' which is either -1 or 1; qfac is
1027 stored in the otherwise unused pixdim[0]. If pixdim[0]=0.0 (which
1028 should not occur), we take qfac=1. Of course, pixdim[0] is only used
1029 when reading a NIFTI-1 header, not when reading an ANALYZE 7.5 header.
1030
1031 N.B.: The units of (x,y,z) can be specified using the xyzt_units field.
1032
1033 METHOD 1 (the "old" way, used only when qform_code = 0):
1034 -------------------------------------------------------
1035 The coordinate mapping from (i,j,k) to (x,y,z) is the ANALYZE
1036 7.5 way. This is a simple scaling relationship:
1037
1038 x = pixdim[1] * i
1039 y = pixdim[2] * j
1040 z = pixdim[3] * k
1041
1042 No particular spatial orientation is attached to these (x,y,z)
1043 coordinates. (NIFTI-1 does not have the ANALYZE 7.5 orient field,
1044 which is not general and is often not set properly.) This method
1045 is not recommended, and is present mainly for compatibility with
1046 ANALYZE 7.5 files.
1047
1048 METHOD 2 (used when qform_code > 0, which should be the "normal" case):
1049 ---------------------------------------------------------------------
1050 The (x,y,z) coordinates are given by the pixdim[] scales, a rotation
1051 matrix, and a shift. This method is intended to represent
1052 "scanner-anatomical" coordinates, which are often embedded in the
1053 image header (e.g., DICOM fields (0020,0032), (0020,0037), (0028,0030),
1054 and (0018,0050)), and represent the nominal orientation and location of
1055 the data. This method can also be used to represent "aligned"
1056 coordinates, which would typically result from some post-acquisition
1057 alignment of the volume to a standard orientation (e.g., the same
1058 subject on another day, or a rigid rotation to true anatomical
1059 orientation from the tilted position of the subject in the scanner).
1060 The formula for (x,y,z) in terms of header parameters and (i,j,k) is:
1061
1062 [ x ] [ R11 R12 R13 ] [ pixdim[1] * i ] [ qoffset_x ]
1063 [ y ] = [ R21 R22 R23 ] [ pixdim[2] * j ] + [ qoffset_y ]
1064 [ z ] [ R31 R32 R33 ] [ qfac * pixdim[3] * k ] [ qoffset_z ]
1065
1066 The qoffset_* shifts are in the NIFTI-1 header. Note that the center
1067 of the (i,j,k)=(0,0,0) voxel (first value in the dataset array) is
1068 just (x,y,z)=(qoffset_x,qoffset_y,qoffset_z).
1069
1070 The rotation matrix R is calculated from the quatern_* parameters.
1071 This calculation is described below.
1072
1073 The scaling factor qfac is either 1 or -1. The rotation matrix R
1074 defined by the quaternion parameters is "proper" (has determinant 1).
1075 This may not fit the needs of the data; for example, if the image
1076 grid is
1077 i increases from Left-to-Right
1078 j increases from Anterior-to-Posterior
1079 k increases from Inferior-to-Superior
1080 Then (i,j,k) is a left-handed triple. In this example, if qfac=1,
1081 the R matrix would have to be
1082
1083 [ 1 0 0 ]
1084 [ 0 -1 0 ] which is "improper" (determinant = -1).
1085 [ 0 0 1 ]
1086
1087 If we set qfac=-1, then the R matrix would be
1088
1089 [ 1 0 0 ]
1090 [ 0 -1 0 ] which is proper.
1091 [ 0 0 -1 ]
1092
1093 This R matrix is represented by quaternion [a,b,c,d] = [0,1,0,0]
1094 (which encodes a 180 degree rotation about the x-axis).
1095
1096 METHOD 3 (used when sform_code > 0):
1097 -----------------------------------
1098 The (x,y,z) coordinates are given by a general affine transformation
1099 of the (i,j,k) indexes:
1100
1101 x = srow_x[0] * i + srow_x[1] * j + srow_x[2] * k + srow_x[3]
1102 y = srow_y[0] * i + srow_y[1] * j + srow_y[2] * k + srow_y[3]
1103 z = srow_z[0] * i + srow_z[1] * j + srow_z[2] * k + srow_z[3]
1104
1105 The srow_* vectors are in the NIFTI_1 header. Note that no use is
1106 made of pixdim[] in this method.
1107
1108 WHY 3 METHODS?
1109 --------------
1110 Method 1 is provided only for backwards compatibility. The intention
1111 is that Method 2 (qform_code > 0) represents the nominal voxel locations
1112 as reported by the scanner, or as rotated to some fiducial orientation and
1113 location. Method 3, if present (sform_code > 0), is to be used to give
1114 the location of the voxels in some standard space. The sform_code
1115 indicates which standard space is present. Both methods 2 and 3 can be
1116 present, and be useful in different contexts (method 2 for displaying the
1117 data on its original grid; method 3 for displaying it on a standard grid).
1118
1119 In this scheme, a dataset would originally be set up so that the
1120 Method 2 coordinates represent what the scanner reported. Later,
1121 a registration to some standard space can be computed and inserted
1122 in the header. Image display software can use either transform,
1123 depending on its purposes and needs.
1124
1125 In Method 2, the origin of coordinates would generally be whatever
1126 the scanner origin is; for example, in MRI, (0,0,0) is the center
1127 of the gradient coil.
1128
1129 In Method 3, the origin of coordinates would depend on the value
1130 of sform_code; for example, for the Talairach coordinate system,
1131 (0,0,0) corresponds to the Anterior Commissure.
1132
1133 QUATERNION REPRESENTATION OF ROTATION MATRIX (METHOD 2)
1134 -------------------------------------------------------
1135 The orientation of the (x,y,z) axes relative to the (i,j,k) axes
1136 in 3D space is specified using a unit quaternion [a,b,c,d], where
1137 a*a+b*b+c*c+d*d=1. The (b,c,d) values are all that is needed, since
1138 we require that a = sqrt(1.0-(b*b+c*c+d*d)) be nonnegative. The (b,c,d)
1139 values are stored in the (quatern_b,quatern_c,quatern_d) fields.
1140
1141 The quaternion representation is chosen for its compactness in
1142 representing rotations. The (proper) 3x3 rotation matrix that
1143 corresponds to [a,b,c,d] is
1144
1145 [ a*a+b*b-c*c-d*d 2*b*c-2*a*d 2*b*d+2*a*c ]
1146 R = [ 2*b*c+2*a*d a*a+c*c-b*b-d*d 2*c*d-2*a*b ]
1147 [ 2*b*d-2*a*c 2*c*d+2*a*b a*a+d*d-c*c-b*b ]
1148
1149 [ R11 R12 R13 ]
1150 = [ R21 R22 R23 ]
1151 [ R31 R32 R33 ]
1152
1153 If (p,q,r) is a unit 3-vector, then rotation of angle h about that
1154 direction is represented by the quaternion
1155
1156 [a,b,c,d] = [cos(h/2), p*sin(h/2), q*sin(h/2), r*sin(h/2)].
1157
1158 Requiring a >= 0 is equivalent to requiring -Pi <= h <= Pi. (Note that
1159 [-a,-b,-c,-d] represents the same rotation as [a,b,c,d]; there are 2
1160 quaternions that can be used to represent a given rotation matrix R.)
1161 To rotate a 3-vector (x,y,z) using quaternions, we compute the
1162 quaternion product
1163
1164 [0,x',y',z'] = [a,b,c,d] * [0,x,y,z] * [a,-b,-c,-d]
1165
1166 which is equivalent to the matrix-vector multiply
1167
1168 [ x' ] [ x ]
1169 [ y' ] = R [ y ] (equivalence depends on a*a+b*b+c*c+d*d=1)
1170 [ z' ] [ z ]
1171
1172 Multiplication of 2 quaternions is defined by the following:
1173
1174 [a,b,c,d] = a*1 + b*I + c*J + d*K
1175 where
1176 I*I = J*J = K*K = -1 (I,J,K are square roots of -1)
1177 I*J = K J*K = I K*I = J
1178 J*I = -K K*J = -I I*K = -J (not commutative!)
1179 For example
1180 [a,b,0,0] * [0,0,0,1] = [0,0,-b,a]
1181 since this expands to
1182 (a+b*I)*(K) = (a*K+b*I*K) = (a*K-b*J).
1183
1184 The above formula shows how to go from quaternion (b,c,d) to
1185 rotation matrix and direction cosines. Conversely, given R,
1186 we can compute the fields for the NIFTI-1 header by
1187
1188 a = 0.5 * sqrt(1+R11+R22+R33) (not stored)
1189 b = 0.25 * (R32-R23) / a => quatern_b
1190 c = 0.25 * (R13-R31) / a => quatern_c
1191 d = 0.25 * (R21-R12) / a => quatern_d
1192
1193 If a=0 (a 180 degree rotation), alternative formulas are needed.
1194 See the nifti1_io.c function mat44_to_quatern() for an implementation
1195 of the various cases in converting R to [a,b,c,d].
1196
1197 Note that R-transpose (= R-inverse) would lead to the quaternion
1198 [a,-b,-c,-d].
1199
1200 The choice to specify the qoffset_x (etc.) values in the final
1201 coordinate system is partly to make it easy to convert DICOM images to
1202 this format. The DICOM attribute "Image Position (Patient)" (0020,0032)
1203 stores the (Xd,Yd,Zd) coordinates of the center of the first voxel.
1204 Here, (Xd,Yd,Zd) refer to DICOM coordinates, and Xd=-x, Yd=-y, Zd=z,
1205 where (x,y,z) refers to the NIFTI coordinate system discussed above.
1206 (i.e., DICOM +Xd is Left, +Yd is Posterior, +Zd is Superior,
1207 whereas +x is Right, +y is Anterior , +z is Superior. )
1208 Thus, if the (0020,0032) DICOM attribute is extracted into (px,py,pz), then
1209 qoffset_x = -px qoffset_y = -py qoffset_z = pz
1210 is a reasonable setting when qform_code=NIFTI_XFORM_SCANNER_ANAT.
1211
1212 That is, DICOM's coordinate system is 180 degrees rotated about the z-axis
1213 from the neuroscience/NIFTI coordinate system. To transform between DICOM
1214 and NIFTI, you just have to negate the x- and y-coordinates.
1215
1216 The DICOM attribute (0020,0037) "Image Orientation (Patient)" gives the
1217 orientation of the x- and y-axes of the image data in terms of 2 3-vectors.
1218 The first vector is a unit vector along the x-axis, and the second is
1219 along the y-axis. If the (0020,0037) attribute is extracted into the
1220 value (xa,xb,xc,ya,yb,yc), then the first two columns of the R matrix
1221 would be
1222 [ -xa -ya ]
1223 [ -xb -yb ]
1224 [ xc yc ]
1225 The negations are because DICOM's x- and y-axes are reversed relative
1226 to NIFTI's. The third column of the R matrix gives the direction of
1227 displacement (relative to the subject) along the slice-wise direction.
1228 This orientation is not encoded in the DICOM standard in a simple way;
1229 DICOM is mostly concerned with 2D images. The third column of R will be
1230 either the cross-product of the first 2 columns or its negative. It is
1231 possible to infer the sign of the 3rd column by examining the coordinates
1232 in DICOM attribute (0020,0032) "Image Position (Patient)" for successive
1233 slices. However, this method occasionally fails for reasons that I
1234 (RW Cox) do not understand.
1235-----------------------------------------------------------------------------*/
1236
1237 /* [qs]form_code value: */ /* x,y,z coordinate system refers to: */
1238 /*-----------------------*/ /*---------------------------------------*/
1239
1246#define NIFTI_XFORM_UNKNOWN 0
1247
1250#define NIFTI_XFORM_SCANNER_ANAT 1
1251
1255#define NIFTI_XFORM_ALIGNED_ANAT 2
1256
1260#define NIFTI_XFORM_TALAIRACH 3
1261
1264#define NIFTI_XFORM_MNI_152 4
1265
1270#define NIFTI_XFORM_TEMPLATE_OTHER 5
1271
1272/* @} */
1273
1274/*---------------------------------------------------------------------------*/
1275/* UNITS OF SPATIAL AND TEMPORAL DIMENSIONS:
1276 ----------------------------------------
1277 The codes below can be used in xyzt_units to indicate the units of pixdim.
1278 As noted earlier, dimensions 1,2,3 are for x,y,z; dimension 4 is for
1279 time (t).
1280 - If dim[4]=1 or dim[0] < 4, there is no time axis.
1281 - A single time series (no space) would be specified with
1282 - dim[0] = 4 (for scalar data) or dim[0] = 5 (for vector data)
1283 - dim[1] = dim[2] = dim[3] = 1
1284 - dim[4] = number of time points
1285 - pixdim[4] = time step
1286 - xyzt_units indicates units of pixdim[4]
1287 - dim[5] = number of values stored at each time point
1288
1289 Bits 0..2 of xyzt_units specify the units of pixdim[1..3]
1290 (e.g., spatial units are values 1..7).
1291 Bits 3..5 of xyzt_units specify the units of pixdim[4]
1292 (e.g., temporal units are multiples of 8).
1293
1294 This compression of 2 distinct concepts into 1 byte is due to the
1295 limited space available in the 348 byte ANALYZE 7.5 header. The
1296 macros XYZT_TO_SPACE and XYZT_TO_TIME can be used to mask off the
1297 undesired bits from the xyzt_units fields, leaving "pure" space
1298 and time codes. Inversely, the macro SPACE_TIME_TO_XYZT can be
1299 used to assemble a space code (0,1,2,...,7) with a time code
1300 (0,8,16,32,...,56) into the combined value for xyzt_units.
1301
1302 Note that codes are provided to indicate the "time" axis units are
1303 actually frequency in Hertz (_HZ), in part-per-million (_PPM)
1304 or in radians-per-second (_RADS).
1305
1306 The toffset field can be used to indicate a nonzero start point for
1307 the time axis. That is, time point #m is at t=toffset+m*pixdim[4]
1308 for m=0..dim[4]-1.
1309-----------------------------------------------------------------------------*/
1310
1317#define NIFTI_UNITS_UNKNOWN 0
1318
1321#define NIFTI_UNITS_METER 1
1323#define NIFTI_UNITS_MM 2
1325#define NIFTI_UNITS_MICRON 3
1326
1329#define NIFTI_UNITS_SEC 8
1331#define NIFTI_UNITS_MSEC 16
1333#define NIFTI_UNITS_USEC 24
1334
1335 /*** These units are for spectral data: ***/
1337#define NIFTI_UNITS_HZ 32
1339#define NIFTI_UNITS_PPM 40
1341#define NIFTI_UNITS_RADS 48
1342/* @} */
1343
1344#undef XYZT_TO_SPACE
1345#undef XYZT_TO_TIME
1346#define XYZT_TO_SPACE(xyzt) ( (xyzt) & 0x07 )
1347#define XYZT_TO_TIME(xyzt) ( (xyzt) & 0x38 )
1348
1349#undef SPACE_TIME_TO_XYZT
1350#define SPACE_TIME_TO_XYZT(ss,tt) ( (((char)(ss)) & 0x07) \
1351 | (((char)(tt)) & 0x38) )
1352
1353/*---------------------------------------------------------------------------*/
1354/* MRI-SPECIFIC SPATIAL AND TEMPORAL INFORMATION:
1355 ---------------------------------------------
1356 A few fields are provided to store some extra information
1357 that is sometimes important when storing the image data
1358 from an FMRI time series experiment. (After processing such
1359 data into statistical images, these fields are not likely
1360 to be useful.)
1361
1362 { freq_dim } = These fields encode which spatial dimension (1,2, or 3)
1363 { phase_dim } = corresponds to which acquisition dimension for MRI data.
1364 { slice_dim } =
1365 Examples:
1366 Rectangular scan multi-slice EPI:
1367 freq_dim = 1 phase_dim = 2 slice_dim = 3 (or some permutation)
1368 Spiral scan multi-slice EPI:
1369 freq_dim = phase_dim = 0 slice_dim = 3
1370 since the concepts of frequency- and phase-encoding directions
1371 don't apply to spiral scan
1372
1373 slice_duration = If this is positive, AND if slice_dim is nonzero,
1374 indicates the amount of time used to acquire 1 slice.
1375 slice_duration*dim[slice_dim] can be less than pixdim[4]
1376 with a clustered acquisition method, for example.
1377
1378 slice_code = If this is nonzero, AND if slice_dim is nonzero, AND
1379 if slice_duration is positive, indicates the timing
1380 pattern of the slice acquisition. The following codes
1381 are defined:
1382 NIFTI_SLICE_SEQ_INC == sequential increasing
1383 NIFTI_SLICE_SEQ_DEC == sequential decreasing
1384 NIFTI_SLICE_ALT_INC == alternating increasing
1385 NIFTI_SLICE_ALT_DEC == alternating decreasing
1386 NIFTI_SLICE_ALT_INC2 == alternating increasing #2
1387 NIFTI_SLICE_ALT_DEC2 == alternating decreasing #2
1388 { slice_start } = Indicates the start and end of the slice acquisition
1389 { slice_end } = pattern, when slice_code is nonzero. These values
1390 are present to allow for the possible addition of
1391 "padded" slices at either end of the volume, which
1392 don't fit into the slice timing pattern. If there
1393 are no padding slices, then slice_start=0 and
1394 slice_end=dim[slice_dim]-1 are the correct values.
1395 For these values to be meaningful, slice_start must
1396 be non-negative and slice_end must be greater than
1397 slice_start. Otherwise, they should be ignored.
1398
1399 The following table indicates the slice timing pattern, relative to
1400 time=0 for the first slice acquired, for some sample cases. Here,
1401 dim[slice_dim]=7 (there are 7 slices, labeled 0..6), slice_duration=0.1,
1402 and slice_start=1, slice_end=5 (1 padded slice on each end).
1403
1404 slice
1405 index SEQ_INC SEQ_DEC ALT_INC ALT_DEC ALT_INC2 ALT_DEC2
1406 6 : n/a n/a n/a n/a n/a n/a n/a = not applicable
1407 5 : 0.4 0.0 0.2 0.0 0.4 0.2 (slice time offset
1408 4 : 0.3 0.1 0.4 0.3 0.1 0.0 doesn't apply to
1409 3 : 0.2 0.2 0.1 0.1 0.3 0.3 slices outside
1410 2 : 0.1 0.3 0.3 0.4 0.0 0.1 the range
1411 1 : 0.0 0.4 0.0 0.2 0.2 0.4 slice_start ..
1412 0 : n/a n/a n/a n/a n/a n/a slice_end)
1413
1414 The SEQ slice_codes are sequential ordering (uncommon but not unknown),
1415 either increasing in slice number or decreasing (INC or DEC), as
1416 illustrated above.
1417
1418 The ALT slice codes are alternating ordering. The 'standard' way for
1419 these to operate (without the '2' on the end) is for the slice timing
1420 to start at the edge of the slice_start .. slice_end group (at slice_start
1421 for INC and at slice_end for DEC). For the 'ALT_*2' slice_codes, the
1422 slice timing instead starts at the first slice in from the edge (at
1423 slice_start+1 for INC2 and at slice_end-1 for DEC2). This latter
1424 acquisition scheme is found on some Siemens scanners.
1425
1426 The fields freq_dim, phase_dim, slice_dim are all squished into the single
1427 byte field dim_info (2 bits each, since the values for each field are
1428 limited to the range 0..3). This unpleasantness is due to lack of space
1429 in the 348 byte allowance.
1430
1431 The macros DIM_INFO_TO_FREQ_DIM, DIM_INFO_TO_PHASE_DIM, and
1432 DIM_INFO_TO_SLICE_DIM can be used to extract these values from the
1433 dim_info byte.
1434
1435 The macro FPS_INTO_DIM_INFO can be used to put these 3 values
1436 into the dim_info byte.
1437-----------------------------------------------------------------------------*/
1438
1439#undef DIM_INFO_TO_FREQ_DIM
1440#undef DIM_INFO_TO_PHASE_DIM
1441#undef DIM_INFO_TO_SLICE_DIM
1442
1443#define DIM_INFO_TO_FREQ_DIM(di) ( ((di) ) & 0x03 )
1444#define DIM_INFO_TO_PHASE_DIM(di) ( ((di) >> 2) & 0x03 )
1445#define DIM_INFO_TO_SLICE_DIM(di) ( ((di) >> 4) & 0x03 )
1446
1447#undef FPS_INTO_DIM_INFO
1448#define FPS_INTO_DIM_INFO(fd,pd,sd) ( ( ( ((char)(fd)) & 0x03) ) | \
1449 ( ( ((char)(pd)) & 0x03) << 2 ) | \
1450 ( ( ((char)(sd)) & 0x03) << 4 ) )
1451
1457#define NIFTI_SLICE_UNKNOWN 0
1458#define NIFTI_SLICE_SEQ_INC 1
1459#define NIFTI_SLICE_SEQ_DEC 2
1460#define NIFTI_SLICE_ALT_INC 3
1461#define NIFTI_SLICE_ALT_DEC 4
1462#define NIFTI_SLICE_ALT_INC2 5 /* 05 May 2005: RWCox */
1463#define NIFTI_SLICE_ALT_DEC2 6 /* 05 May 2005: RWCox */
1464/* @} */
1465
1466/*---------------------------------------------------------------------------*/
1467/* UNUSED FIELDS:
1468 -------------
1469 Some of the ANALYZE 7.5 fields marked as ++UNUSED++ may need to be set
1470 to particular values for compatibility with other programs. The issue
1471 of interoperability of ANALYZE 7.5 files is a murky one -- not all
1472 programs require exactly the same set of fields. (Unobscuring this
1473 murkiness is a principal motivation behind NIFTI-1.)
1474
1475 Some of the fields that may need to be set for other (non-NIFTI aware)
1476 software to be happy are:
1477
1478 extents dbh.h says this should be 16384
1479 regular dbh.h says this should be the character 'r'
1480 glmin, } dbh.h says these values should be the min and max voxel
1481 glmax } values for the entire dataset
1482
1483 It is best to initialize ALL fields in the NIFTI-1 header to 0
1484 (e.g., with calloc()), then fill in what is needed.
1485-----------------------------------------------------------------------------*/
1486
1487/*---------------------------------------------------------------------------*/
1488/* MISCELLANEOUS C MACROS
1489-----------------------------------------------------------------------------*/
1490
1491/*.................*/
1495#define NIFTI_VERSION(h) \
1496 ( ( (h).magic[0]=='n' && (h).magic[3]=='\0' && \
1497 ( (h).magic[1]=='i' || (h).magic[1]=='+' ) && \
1498 ( (h).magic[2]>='1' && (h).magic[2]<='9' ) ) \
1499 ? (h).magic[2]-'0' : 0 )
1500
1501/*.................*/
1506#define NIFTI_ONEFILE(h) ( (h).magic[1] == '+' )
1507
1508/*.................*/
1512#define NIFTI_NEEDS_SWAP(h) ( (h).dim[0] < 0 || (h).dim[0] > 7 )
1513
1514/*.................*/
1518#define NIFTI_5TH_DIM(h) ( ((h).dim[0]>4 && (h).dim[5]>1) ? (h).dim[5] : 0 )
1519
1520/*****************************************************************************/
1521
1522/*=================*/
1523#ifdef __cplusplus
1524}
1525#endif
1526/*=================*/
1527
1528#endif /* _NIFTI_HEADER_ */
short intent_code
Definition nifti1.h:168
float srow_y[4]
Definition nifti1.h:201
int glmax
Definition nifti1.h:183
float toffset
Definition nifti1.h:182
char db_name[18]
Definition nifti1.h:154
short session_error
Definition nifti1.h:156
short slice_end
Definition nifti1.h:176
float quatern_c
Definition nifti1.h:194
char data_type[10]
Definition nifti1.h:153
float scl_slope
Definition nifti1.h:174
short sform_code
Definition nifti1.h:191
float quatern_b
Definition nifti1.h:193
char * edata
Definition nifti1.h:300
char magic[4]
Definition nifti1.h:206
float intent_p1
Definition nifti1.h:162
float qoffset_y
Definition nifti1.h:197
float cal_min
Definition nifti1.h:180
short bitpix
Definition nifti1.h:170
char xyzt_units
Definition nifti1.h:178
float qoffset_x
Definition nifti1.h:196
float slice_duration
Definition nifti1.h:181
char dim_info
Definition nifti1.h:158
char descrip[80]
Definition nifti1.h:187
char aux_file[24]
Definition nifti1.h:188
short qform_code
Definition nifti1.h:190
float qoffset_z
Definition nifti1.h:198
float intent_p3
Definition nifti1.h:166
float vox_offset
Definition nifti1.h:173
int esize
Definition nifti1.h:298
int ecode
Definition nifti1.h:299
int extents
Definition nifti1.h:155
float intent_p2
Definition nifti1.h:164
short dim[8]
Definition nifti1.h:161
float scl_inter
Definition nifti1.h:175
int glmin
Definition nifti1.h:184
char regular
Definition nifti1.h:157
short datatype
Definition nifti1.h:169
float srow_x[4]
Definition nifti1.h:200
short slice_start
Definition nifti1.h:171
char intent_name[16]
Definition nifti1.h:204
float srow_z[4]
Definition nifti1.h:202
int sizeof_hdr
Definition nifti1.h:152
char slice_code
Definition nifti1.h:177
float pixdim[8]
Definition nifti1.h:172
float cal_max
Definition nifti1.h:179
float quatern_d
Definition nifti1.h:195
This structure represents a 4-byte string that should follow the binary nifti_1_header data in a NIFT...
Definition nifti1.h:291
Data structure defining the fields of a header extension.
Definition nifti1.h:297
Data structure defining the fields in the nifti1 header. This binary header should be found at the be...
Definition nifti1.h:148