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nifti1.h

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00001 
00012 #ifndef _NIFTI_HEADER_
00013 #define _NIFTI_HEADER_
00014 
00015 /*****************************************************************************
00016       ** This file defines the "NIFTI-1" header format.               **
00017       ** It is derived from 2 meetings at the NIH (31 Mar 2003 and    **
00018       ** 02 Sep 2003) of the Data Format Working Group (DFWG),        **
00019       ** chartered by the NIfTI (Neuroimaging Informatics Technology  **
00020       ** Initiative) at the National Institutes of Health (NIH).      **
00021       **--------------------------------------------------------------**
00022       ** Neither the National Institutes of Health (NIH), the DFWG,   **
00023       ** nor any of the members or employees of these institutions    **
00024       ** imply any warranty of usefulness of this material for any    **
00025       ** purpose, and do not assume any liability for damages,        **
00026       ** incidental or otherwise, caused by any use of this document. **
00027       ** If these conditions are not acceptable, do not use this!     **
00028       **--------------------------------------------------------------**
00029       ** Author:   Robert W Cox (NIMH, Bethesda)                      **
00030       ** Advisors: John Ashburner (FIL, London),                      **
00031       **           Stephen Smith (FMRIB, Oxford),                     **
00032       **           Mark Jenkinson (FMRIB, Oxford)                     **
00033 ******************************************************************************/
00034 
00035 /*---------------------------------------------------------------------------*/
00036 /* Note that the ANALYZE 7.5 file header (dbh.h) is
00037          (c) Copyright 1986-1995
00038          Biomedical Imaging Resource
00039          Mayo Foundation
00040    Incorporation of components of dbh.h are by permission of the
00041    Mayo Foundation.
00042 
00043    Changes from the ANALYZE 7.5 file header in this file are released to the
00044    public domain, including the functional comments and any amusing asides.
00045 -----------------------------------------------------------------------------*/
00046 
00047 /*---------------------------------------------------------------------------*/
00115 /*---------------------------------------------------------------------------*/
00116 /* HEADER STRUCT DECLARATION:
00117    -------------------------
00118    In the comments below for each field, only NIFTI-1 specific requirements
00119    or changes from the ANALYZE 7.5 format are described.  For convenience,
00120    the 348 byte header is described as a single struct, rather than as the
00121    ANALYZE 7.5 group of 3 substructs.
00122 
00123    Further comments about the interpretation of various elements of this
00124    header are after the data type definition itself.  Fields that are
00125    marked as ++UNUSED++ have no particular interpretation in this standard.
00126    (Also see the UNUSED FIELDS comment section, far below.)
00127 
00128    The presumption below is that the various C types have particular sizes:
00129      sizeof(int) = sizeof(float) = 4 ;  sizeof(short) = 2
00130 -----------------------------------------------------------------------------*/
00131 
00132 /*=================*/
00133 #ifdef  __cplusplus
00134 extern "C" {
00135 #endif
00136 /*=================*/
00137 
00143                         /*************************/  /************************/
00144 struct nifti_1_header { /* NIFTI-1 usage         */  /* ANALYZE 7.5 field(s) */
00145                         /*************************/  /************************/
00146 
00147                                            /*--- was header_key substruct ---*/
00148  int   sizeof_hdr;      /* int sizeof_hdr;      */
00149  char  data_type[10];   /* char data_type[10];  */
00150  char  db_name[18];     /* char db_name[18];    */
00151  int   extents;         /* int extents;         */
00152  short session_error;   /* short session_error; */
00153  char  regular;         /* char regular;        */
00154  char  dim_info;        /* char hkey_un0;       */
00155 
00156                                       /*--- was image_dimension substruct ---*/
00157  short dim[8];          /* short dim[8];        */
00158  float intent_p1 ;      /* short unused8;       */
00159                                                      /* short unused9;       */
00160  float intent_p2 ;      /* short unused10;      */
00161                                                      /* short unused11;      */
00162  float intent_p3 ;      /* short unused12;      */
00163                                                      /* short unused13;      */
00164  short intent_code ;    /* short unused14;      */
00165  short datatype;        /* short datatype;      */
00166  short bitpix;          /* short bitpix;        */
00167  short slice_start;     /* short dim_un0;       */
00168  float pixdim[8];       /* float pixdim[8];     */
00169  float vox_offset;      /* float vox_offset;    */
00170  float scl_slope ;      /* float funused1;      */
00171  float scl_inter ;      /* float funused2;      */
00172  short slice_end;       /* float funused3;      */
00173  char  slice_code ;   
00174  char  xyzt_units ;   
00175  float cal_max;         /* float cal_max;       */
00176  float cal_min;         /* float cal_min;       */
00177  float slice_duration;  /* float compressed;    */
00178  float toffset;         /* float verified;      */
00179  int   glmax;           /* int glmax;           */
00180  int   glmin;           /* int glmin;           */
00181 
00182                                          /*--- was data_history substruct ---*/
00183  char  descrip[80];     /* char descrip[80];    */
00184  char  aux_file[24];    /* char aux_file[24];   */
00185 
00186  short qform_code ;     /*-- all ANALYZE 7.5 ---*/
00187  short sform_code ;     /*   fields below here  */
00188                                                      /*   are replaced       */
00189  float quatern_b ;    
00190  float quatern_c ;    
00191  float quatern_d ;    
00192  float qoffset_x ;    
00193  float qoffset_y ;    
00194  float qoffset_z ;    
00196  float srow_x[4] ;    
00197  float srow_y[4] ;    
00198  float srow_z[4] ;    
00200  char intent_name[16];
00202  char magic[4] ;      
00204 } ;                   /**** 348 bytes total ****/
00205 
00206 typedef struct nifti_1_header nifti_1_header ;
00207 
00208 /*---------------------------------------------------------------------------*/
00209 /* HEADER EXTENSIONS:
00210    -----------------
00211    After the end of the 348 byte header (e.g., after the magic field),
00212    the next 4 bytes are a char array field named "extension". By default,
00213    all 4 bytes of this array should be set to zero. In a .nii file, these
00214    4 bytes will always be present, since the earliest start point for
00215    the image data is byte #352. In a separate .hdr file, these bytes may
00216    or may not be present. If not present (i.e., if the length of the .hdr
00217    file is 348 bytes), then a NIfTI-1 compliant program should use the
00218    default value of extension={0,0,0,0}. The first byte (extension[0])
00219    is the only value of this array that is specified at present. The other
00220    3 bytes are reserved for future use.
00221 
00222    If extension[0] is nonzero, it indicates that extended header information
00223    is present in the bytes following the extension array. In a .nii file,
00224    this extended header data is before the image data (and vox_offset
00225    must be set correctly to allow for this). In a .hdr file, this extended
00226    data follows extension and proceeds (potentially) to the end of the file.
00227 
00228    The format of extended header data is weakly specified. Each extension
00229    must be an integer multiple of 16 bytes long. The first 8 bytes of each
00230    extension comprise 2 integers:
00231       int esize , ecode ;
00232    These values may need to be byte-swapped, as indicated by dim[0] for
00233    the rest of the header.
00234      * esize is the number of bytes that form the extended header data
00235        + esize must be a positive integral multiple of 16
00236        + this length includes the 8 bytes of esize and ecode themselves
00237      * ecode is a non-negative integer that indicates the format of the
00238        extended header data that follows
00239        + different ecode values are assigned to different developer groups
00240        + at present, the "registered" values for code are
00241          = 0 = unknown private format (not recommended!)
00242          = 2 = DICOM format (i.e., attribute tags and values)
00243          = 4 = AFNI group (i.e., ASCII XML-ish elements)
00244    In the interests of interoperability (a primary rationale for NIfTI),
00245    groups developing software that uses this extension mechanism are
00246    encouraged to document and publicize the format of their extensions.
00247    To this end, the NIfTI DFWG will assign even numbered codes upon request
00248    to groups submitting at least rudimentary documentation for the format
00249    of their extension; at present, the contact is mailto:rwcox@nih.gov.
00250    The assigned codes and documentation will be posted on the NIfTI
00251    website. All odd values of ecode (and 0) will remain unassigned;
00252    at least, until the even ones are used up, when we get to 2,147,483,646.
00253 
00254    Note that the other contents of the extended header data section are
00255    totally unspecified by the NIfTI-1 standard. In particular, if binary
00256    data is stored in such a section, its byte order is not necessarily
00257    the same as that given by examining dim[0]; it is incumbent on the
00258    programs dealing with such data to determine the byte order of binary
00259    extended header data.
00260 
00261    Multiple extended header sections are allowed, each starting with an
00262    esize,ecode value pair. The first esize value, as described above,
00263    is at bytes #352-355 in the .hdr or .nii file (files start at byte #0).
00264    If this value is positive, then the second (esize2) will be found
00265    starting at byte #352+esize1 , the third (esize3) at byte #352+esize1+esize2,
00266    et cetera.  Of course, in a .nii file, the value of vox_offset must
00267    be compatible with these extensions. If a malformed file indicates
00268    that an extended header data section would run past vox_offset, then
00269    the entire extended header section should be ignored. In a .hdr file,
00270    if an extended header data section would run past the end-of-file,
00271    that extended header data should also be ignored.
00272 
00273    With the above scheme, a program can successively examine the esize
00274    and ecode values, and skip over each extended header section if the
00275    program doesn't know how to interpret the data within. Of course, any
00276    program can simply ignore all extended header sections simply by jumping
00277    straight to the image data using vox_offset.
00278 -----------------------------------------------------------------------------*/
00279    
00287 struct nifti1_extender { char extension[4] ; } ;
00288 typedef struct nifti1_extender nifti1_extender ;
00289 
00293 struct nifti1_extension {
00294    int    esize ; 
00295    int    ecode ; 
00296    char * edata ; 
00297 } ;
00298 typedef struct nifti1_extension nifti1_extension ;
00299 
00300 /*---------------------------------------------------------------------------*/
00301 /* DATA DIMENSIONALITY (as in ANALYZE 7.5):
00302    ---------------------------------------
00303      dim[0] = number of dimensions;
00304               - if dim[0] is outside range 1..7, then the header information
00305                 needs to be byte swapped appropriately
00306               - ANALYZE supports dim[0] up to 7, but NIFTI-1 reserves
00307                 dimensions 1,2,3 for space (x,y,z), 4 for time (t), and
00308                 5,6,7 for anything else needed.
00309 
00310      dim[i] = length of dimension #i, for i=1..dim[0]  (must be positive)
00311               - also see the discussion of intent_code, far below
00312 
00313      pixdim[i] = voxel width along dimension #i, i=1..dim[0] (positive)
00314                  - cf. ORIENTATION section below for use of pixdim[0]
00315                  - the units of pixdim can be specified with the xyzt_units
00316                    field (also described far below).
00317 
00318    Number of bits per voxel value is in bitpix, which MUST correspond with
00319    the datatype field.  The total number of bytes in the image data is
00320      dim[1] * ... * dim[dim[0]] * bitpix / 8
00321 
00322    In NIFTI-1 files, dimensions 1,2,3 are for space, dimension 4 is for time,
00323    and dimension 5 is for storing multiple values at each spatiotemporal
00324    voxel.  Some examples:
00325      - A typical whole-brain FMRI experiment's time series:
00326         - dim[0] = 4
00327         - dim[1] = 64   pixdim[1] = 3.75 xyzt_units =  NIFTI_UNITS_MM
00328         - dim[2] = 64   pixdim[2] = 3.75             | NIFTI_UNITS_SEC
00329         - dim[3] = 20   pixdim[3] = 5.0
00330         - dim[4] = 120  pixdim[4] = 2.0
00331      - A typical T1-weighted anatomical volume:
00332         - dim[0] = 3
00333         - dim[1] = 256  pixdim[1] = 1.0  xyzt_units = NIFTI_UNITS_MM
00334         - dim[2] = 256  pixdim[2] = 1.0
00335         - dim[3] = 128  pixdim[3] = 1.1
00336      - A single slice EPI time series:
00337         - dim[0] = 4
00338         - dim[1] = 64   pixdim[1] = 3.75 xyzt_units =  NIFTI_UNITS_MM
00339         - dim[2] = 64   pixdim[2] = 3.75             | NIFTI_UNITS_SEC
00340         - dim[3] = 1    pixdim[3] = 5.0
00341         - dim[4] = 1200 pixdim[4] = 0.2
00342      - A 3-vector stored at each point in a 3D volume:
00343         - dim[0] = 5
00344         - dim[1] = 256  pixdim[1] = 1.0  xyzt_units = NIFTI_UNITS_MM
00345         - dim[2] = 256  pixdim[2] = 1.0
00346         - dim[3] = 128  pixdim[3] = 1.1
00347         - dim[4] = 1    pixdim[4] = 0.0
00348         - dim[5] = 3                     intent_code = NIFTI_INTENT_VECTOR
00349      - A single time series with a 3x3 matrix at each point:
00350         - dim[0] = 5
00351         - dim[1] = 1                     xyzt_units = NIFTI_UNITS_SEC
00352         - dim[2] = 1
00353         - dim[3] = 1
00354         - dim[4] = 1200 pixdim[4] = 0.2
00355         - dim[5] = 9                     intent_code = NIFTI_INTENT_GENMATRIX
00356         - intent_p1 = intent_p2 = 3.0    (indicates matrix dimensions)
00357 -----------------------------------------------------------------------------*/
00358 
00359 /*---------------------------------------------------------------------------*/
00360 /* DATA STORAGE:
00361    ------------
00362    If the magic field is "n+1", then the voxel data is stored in the
00363    same file as the header.  In this case, the voxel data starts at offset
00364    (int)vox_offset into the header file.  Thus, vox_offset=352.0 means that
00365    the data starts immediately after the NIFTI-1 header.  If vox_offset is
00366    greater than 352, the NIFTI-1 format does not say much about the
00367    contents of the dataset file between the end of the header and the
00368    start of the data.
00369 
00370    FILES:
00371    -----
00372    If the magic field is "ni1", then the voxel data is stored in the
00373    associated ".img" file, starting at offset 0 (i.e., vox_offset is not
00374    used in this case, and should be set to 0.0).
00375 
00376    When storing NIFTI-1 datasets in pairs of files, it is customary to name
00377    the files in the pattern "name.hdr" and "name.img", as in ANALYZE 7.5.
00378    When storing in a single file ("n+1"), the file name should be in
00379    the form "name.nii" (the ".nft" and ".nif" suffixes are already taken;
00380    cf. http://www.icdatamaster.com/n.html ).
00381 
00382    BYTE ORDERING:
00383    -------------
00384    The byte order of the data arrays is presumed to be the same as the byte
00385    order of the header (which is determined by examining dim[0]).
00386 
00387    Floating point types are presumed to be stored in IEEE-754 format.
00388 -----------------------------------------------------------------------------*/
00389 
00390 /*---------------------------------------------------------------------------*/
00391 /* DETAILS ABOUT vox_offset:
00392    ------------------------
00393    In a .nii file, the vox_offset field value is interpreted as the start
00394    location of the image data bytes in that file. In a .hdr/.img file pair,
00395    the vox_offset field value is the start location of the image data
00396    bytes in the .img file.
00397     * If vox_offset is less than 352 in a .nii file, it is equivalent
00398       to 352 (i.e., image data never starts before byte #352 in a .nii file).
00399     * The default value for vox_offset in a .nii file is 352.
00400     * In a .hdr file, the default value for vox_offset is 0.
00401     * vox_offset should be an integer multiple of 16; otherwise, some
00402       programs may not work properly (e.g., SPM). This is to allow
00403       memory-mapped input to be properly byte-aligned.
00404    Note that since vox_offset is an IEEE-754 32 bit float (for compatibility
00405    with the ANALYZE-7.5 format), it effectively has a 24 bit mantissa. All
00406    integers from 0 to 2^24 can be represented exactly in this format, but not
00407    all larger integers are exactly storable as IEEE-754 32 bit floats. However,
00408    unless you plan to have vox_offset be potentially larger than 16 MB, this
00409    should not be an issue. (Actually, any integral multiple of 16 up to 2^27
00410    can be represented exactly in this format, which allows for up to 128 MB
00411    of random information before the image data.  If that isn't enough, then
00412    perhaps this format isn't right for you.)
00413 
00414    In a .img file (i.e., image data stored separately from the NIfTI-1
00415    header), data bytes between #0 and #vox_offset-1 (inclusive) are completely
00416    undefined and unregulated by the NIfTI-1 standard. One potential use of
00417    having vox_offset > 0 in the .hdr/.img file pair storage method is to make
00418    the .img file be a copy of (or link to) a pre-existing image file in some
00419    other format, such as DICOM; then vox_offset would be set to the offset of
00420    the image data in this file. (It may not be possible to follow the
00421    "multiple-of-16 rule" with an arbitrary external file; using the NIfTI-1
00422    format in such a case may lead to a file that is incompatible with software
00423    that relies on vox_offset being a multiple of 16.)
00424 
00425    In a .nii file, data bytes between #348 and #vox_offset-1 (inclusive) may
00426    be used to store user-defined extra information; similarly, in a .hdr file,
00427    any data bytes after byte #347 are available for user-defined extra
00428    information. The (very weak) regulation of this extra header data is
00429    described elsewhere.
00430 -----------------------------------------------------------------------------*/
00431 
00432 /*---------------------------------------------------------------------------*/
00433 /* DATA SCALING:
00434    ------------
00435    If the scl_slope field is nonzero, then each voxel value in the dataset
00436    should be scaled as
00437       y = scl_slope * x + scl_inter
00438    where x = voxel value stored
00439          y = "true" voxel value
00440    Normally, we would expect this scaling to be used to store "true" floating
00441    values in a smaller integer datatype, but that is not required.  That is,
00442    it is legal to use scaling even if the datatype is a float type (crazy,
00443    perhaps, but legal).
00444     - However, the scaling is to be ignored if datatype is DT_RGB24.
00445     - If datatype is a complex type, then the scaling is to be
00446       applied to both the real and imaginary parts.
00447 
00448    The cal_min and cal_max fields (if nonzero) are used for mapping (possibly
00449    scaled) dataset values to display colors:
00450     - Minimum display intensity (black) corresponds to dataset value cal_min.
00451     - Maximum display intensity (white) corresponds to dataset value cal_max.
00452     - Dataset values below cal_min should display as black also, and values
00453       above cal_max as white.
00454     - Colors "black" and "white", of course, may refer to any scalar display
00455       scheme (e.g., a color lookup table specified via aux_file).
00456     - cal_min and cal_max only make sense when applied to scalar-valued
00457       datasets (i.e., dim[0] < 5 or dim[5] = 1).
00458 -----------------------------------------------------------------------------*/
00459 
00460 /*---------------------------------------------------------------------------*/
00461 /* TYPE OF DATA (acceptable values for datatype field):
00462    ---------------------------------------------------
00463    Values of datatype smaller than 256 are ANALYZE 7.5 compatible.
00464    Larger values are NIFTI-1 additions.  These are all multiples of 256, so
00465    that no bits below position 8 are set in datatype.  But there is no need
00466    to use only powers-of-2, as the original ANALYZE 7.5 datatype codes do.
00467 
00468    The additional codes are intended to include a complete list of basic
00469    scalar types, including signed and unsigned integers from 8 to 64 bits,
00470    floats from 32 to 128 bits, and complex (float pairs) from 64 to 256 bits.
00471 
00472    Note that most programs will support only a few of these datatypes!
00473    A NIFTI-1 program should fail gracefully (e.g., print a warning message)
00474    when it encounters a dataset with a type it doesn't like.
00475 -----------------------------------------------------------------------------*/
00476 
00477 #undef DT_UNKNOWN  /* defined in dirent.h on some Unix systems */
00478 
00483                             /*--- the original ANALYZE 7.5 type codes ---*/
00484 #define DT_NONE                    0
00485 #define DT_UNKNOWN                 0     /* what it says, dude           */
00486 #define DT_BINARY                  1     /* binary (1 bit/voxel)         */
00487 #define DT_UNSIGNED_CHAR           2     /* unsigned char (8 bits/voxel) */
00488 #define DT_SIGNED_SHORT            4     /* signed short (16 bits/voxel) */
00489 #define DT_SIGNED_INT              8     /* signed int (32 bits/voxel)   */
00490 #define DT_FLOAT                  16     /* float (32 bits/voxel)        */
00491 #define DT_COMPLEX                32     /* complex (64 bits/voxel)      */
00492 #define DT_DOUBLE                 64     /* double (64 bits/voxel)       */
00493 #define DT_RGB                   128     /* RGB triple (24 bits/voxel)   */
00494 #define DT_ALL                   255     /* not very useful (?)          */
00495 
00496                             /*----- another set of names for the same ---*/
00497 #define DT_UINT8                   2
00498 #define DT_INT16                   4
00499 #define DT_INT32                   8
00500 #define DT_FLOAT32                16
00501 #define DT_COMPLEX64              32
00502 #define DT_FLOAT64                64
00503 #define DT_RGB24                 128
00504 
00505                             /*------------------- new codes for NIFTI ---*/
00506 #define DT_INT8                  256     /* signed char (8 bits)         */
00507 #define DT_UINT16                512     /* unsigned short (16 bits)     */
00508 #define DT_UINT32                768     /* unsigned int (32 bits)       */
00509 #define DT_INT64                1024     /* long long (64 bits)          */
00510 #define DT_UINT64               1280     /* unsigned long long (64 bits) */
00511 #define DT_FLOAT128             1536     /* long double (128 bits)       */
00512 #define DT_COMPLEX128           1792     /* double pair (128 bits)       */
00513 #define DT_COMPLEX256           2048     /* long double pair (256 bits)  */
00514 #define DT_RGBA32               2304     /* 4 byte RGBA (32 bits/voxel)  */
00515 /* @} */
00516 
00517 
00518                             /*------- aliases for all the above codes ---*/
00519 
00525 #define NIFTI_TYPE_UINT8           2
00526 
00527 #define NIFTI_TYPE_INT16           4
00528 
00529 #define NIFTI_TYPE_INT32           8
00530 
00531 #define NIFTI_TYPE_FLOAT32        16
00532 
00533 #define NIFTI_TYPE_COMPLEX64      32
00534 
00535 #define NIFTI_TYPE_FLOAT64        64
00536 
00537 #define NIFTI_TYPE_RGB24         128
00538 
00539 #define NIFTI_TYPE_INT8          256
00540 
00541 #define NIFTI_TYPE_UINT16        512
00542 
00543 #define NIFTI_TYPE_UINT32        768
00544 
00545 #define NIFTI_TYPE_INT64        1024
00546 
00547 #define NIFTI_TYPE_UINT64       1280
00548 
00549 #define NIFTI_TYPE_FLOAT128     1536
00550 
00551 #define NIFTI_TYPE_COMPLEX128   1792
00552 
00553 #define NIFTI_TYPE_COMPLEX256   2048
00554 
00555 #define NIFTI_TYPE_RGBA32       2304
00556 /* @} */
00557 
00558                      /*-------- sample typedefs for complicated types ---*/
00559 #if 0
00560 typedef struct { float       r,i;     } complex_float ;
00561 typedef struct { double      r,i;     } complex_double ;
00562 typedef struct { long double r,i;     } complex_longdouble ;
00563 typedef struct { unsigned char r,g,b; } rgb_byte ;
00564 #endif
00565 
00566 /*---------------------------------------------------------------------------*/
00567 /* INTERPRETATION OF VOXEL DATA:
00568    ----------------------------
00569    The intent_code field can be used to indicate that the voxel data has
00570    some particular meaning.  In particular, a large number of codes is
00571    given to indicate that the the voxel data should be interpreted as
00572    being drawn from a given probability distribution.
00573 
00574    VECTOR-VALUED DATASETS:
00575    ----------------------
00576    The 5th dimension of the dataset, if present (i.e., dim[0]=5 and
00577    dim[5] > 1), contains multiple values (e.g., a vector) to be stored
00578    at each spatiotemporal location.  For example, the header values
00579     - dim[0] = 5
00580     - dim[1] = 64
00581     - dim[2] = 64
00582     - dim[3] = 20
00583     - dim[4] = 1     (indicates no time axis)
00584     - dim[5] = 3
00585     - datatype = DT_FLOAT
00586     - intent_code = NIFTI_INTENT_VECTOR
00587    mean that this dataset should be interpreted as a 3D volume (64x64x20),
00588    with a 3-vector of floats defined at each point in the 3D grid.
00589 
00590    A program reading a dataset with a 5th dimension may want to reformat
00591    the image data to store each voxels' set of values together in a struct
00592    or array.  This programming detail, however, is beyond the scope of the
00593    NIFTI-1 file specification!  Uses of dimensions 6 and 7 are also not
00594    specified here.
00595 
00596    STATISTICAL PARAMETRIC DATASETS (i.e., SPMs):
00597    --------------------------------------------
00598    Values of intent_code from NIFTI_FIRST_STATCODE to NIFTI_LAST_STATCODE
00599    (inclusive) indicate that the numbers in the dataset should be interpreted
00600    as being drawn from a given distribution.  Most such distributions have
00601    auxiliary parameters (e.g., NIFTI_INTENT_TTEST has 1 DOF parameter).
00602 
00603    If the dataset DOES NOT have a 5th dimension, then the auxiliary parameters
00604    are the same for each voxel, and are given in header fields intent_p1,
00605    intent_p2, and intent_p3.
00606 
00607    If the dataset DOES have a 5th dimension, then the auxiliary parameters
00608    are different for each voxel.  For example, the header values
00609     - dim[0] = 5
00610     - dim[1] = 128
00611     - dim[2] = 128
00612     - dim[3] = 1      (indicates a single slice)
00613     - dim[4] = 1      (indicates no time axis)
00614     - dim[5] = 2
00615     - datatype = DT_FLOAT
00616     - intent_code = NIFTI_INTENT_TTEST
00617    mean that this is a 2D dataset (128x128) of t-statistics, with the
00618    t-statistic being in the first "plane" of data and the degrees-of-freedom
00619    parameter being in the second "plane" of data.
00620 
00621    If the dataset 5th dimension is used to store the voxel-wise statistical
00622    parameters, then dim[5] must be 1 plus the number of parameters required
00623    by that distribution (e.g., intent_code=NIFTI_INTENT_TTEST implies dim[5]
00624    must be 2, as in the example just above).
00625 
00626    Note: intent_code values 2..10 are compatible with AFNI 1.5x (which is
00627    why there is no code with value=1, which is obsolescent in AFNI).
00628 
00629    OTHER INTENTIONS:
00630    ----------------
00631    The purpose of the intent_* fields is to help interpret the values
00632    stored in the dataset.  Some non-statistical values for intent_code
00633    and conventions are provided for storing other complex data types.
00634 
00635    The intent_name field provides space for a 15 character (plus 0 byte)
00636    'name' string for the type of data stored. Examples:
00637     - intent_code = NIFTI_INTENT_ESTIMATE; intent_name = "T1";
00638        could be used to signify that the voxel values are estimates of the
00639        NMR parameter T1.
00640     - intent_code = NIFTI_INTENT_TTEST; intent_name = "House";
00641        could be used to signify that the voxel values are t-statistics
00642        for the significance of 'activation' response to a House stimulus.
00643     - intent_code = NIFTI_INTENT_DISPVECT; intent_name = "ToMNI152";
00644        could be used to signify that the voxel values are a displacement
00645        vector that transforms each voxel (x,y,z) location to the
00646        corresponding location in the MNI152 standard brain.
00647     - intent_code = NIFTI_INTENT_SYMMATRIX; intent_name = "DTI";
00648        could be used to signify that the voxel values comprise a diffusion
00649        tensor image.
00650 
00651    If no data name is implied or needed, intent_name[0] should be set to 0.
00652 -----------------------------------------------------------------------------*/
00653 
00656 #define NIFTI_INTENT_NONE        0
00657 
00658     /*-------- These codes are for probability distributions ---------------*/
00659     /* Most distributions have a number of parameters,
00660        below denoted by p1, p2, and p3, and stored in
00661         - intent_p1, intent_p2, intent_p3 if dataset doesn't have 5th dimension
00662         - image data array                if dataset does have 5th dimension
00663 
00664        Functions to compute with many of the distributions below can be found
00665        in the CDF library from U Texas.
00666 
00667        Formulas for and discussions of these distributions can be found in the
00668        following books:
00669 
00670         [U] Univariate Discrete Distributions,
00671             NL Johnson, S Kotz, AW Kemp.
00672 
00673         [C1] Continuous Univariate Distributions, vol. 1,
00674              NL Johnson, S Kotz, N Balakrishnan.
00675 
00676         [C2] Continuous Univariate Distributions, vol. 2,
00677              NL Johnson, S Kotz, N Balakrishnan.                            */
00678     /*----------------------------------------------------------------------*/
00679 
00688 #define NIFTI_INTENT_CORREL      2
00689 
00692 #define NIFTI_INTENT_TTEST       3
00693 
00697 #define NIFTI_INTENT_FTEST       4
00698 
00701 #define NIFTI_INTENT_ZSCORE      5
00702 
00706 #define NIFTI_INTENT_CHISQ       6
00707 
00711 #define NIFTI_INTENT_BETA        7
00712 
00717 #define NIFTI_INTENT_BINOM       8
00718 
00723 #define NIFTI_INTENT_GAMMA       9
00724 
00728 #define NIFTI_INTENT_POISSON    10
00729 
00733 #define NIFTI_INTENT_NORMAL     11
00734 
00739 #define NIFTI_INTENT_FTEST_NONC 12
00740 
00744 #define NIFTI_INTENT_CHISQ_NONC 13
00745 
00750 #define NIFTI_INTENT_LOGISTIC   14
00751 
00756 #define NIFTI_INTENT_LAPLACE    15
00757 
00760 #define NIFTI_INTENT_UNIFORM    16
00761 
00765 #define NIFTI_INTENT_TTEST_NONC 17
00766 
00772 #define NIFTI_INTENT_WEIBULL    18
00773 
00780 #define NIFTI_INTENT_CHI        19
00781 
00787 #define NIFTI_INTENT_INVGAUSS   20
00788 
00793 #define NIFTI_INTENT_EXTVAL     21
00794 
00797 #define NIFTI_INTENT_PVAL       22
00798 
00805 #define NIFTI_INTENT_LOGPVAL    23
00806 
00812 #define NIFTI_INTENT_LOG10PVAL  24
00813 
00816 #define NIFTI_FIRST_STATCODE     2
00817 
00820 #define NIFTI_LAST_STATCODE     24
00821 
00822  /*---------- these values for intent_code aren't for statistics ----------*/
00823 
00828 #define NIFTI_INTENT_ESTIMATE  1001
00829 
00834 #define NIFTI_INTENT_LABEL     1002
00835 
00839 #define NIFTI_INTENT_NEURONAME 1003
00840 
00853 #define NIFTI_INTENT_GENMATRIX 1004
00854 
00866 #define NIFTI_INTENT_SYMMATRIX 1005
00867 
00875 #define NIFTI_INTENT_DISPVECT  1006   /* specifically for displacements */
00876 #define NIFTI_INTENT_VECTOR    1007   /* for any other type of vector */
00877 
00889 #define NIFTI_INTENT_POINTSET  1008
00890 
00902 #define NIFTI_INTENT_TRIANGLE  1009
00903 
00911 #define NIFTI_INTENT_QUATERNION 1010
00912 
00916 #define NIFTI_INTENT_DIMLESS    1011
00917 
00918  /*---------- these values apply to GIFTI datasets ----------*/
00919 
00922 #define NIFTI_INTENT_TIME_SERIES  2001
00923 
00927 #define NIFTI_INTENT_NODE_INDEX   2002
00928 
00938 #define NIFTI_INTENT_RGB_VECTOR   2003
00939 
00949 #define NIFTI_INTENT_RGBA_VECTOR  2004
00950 
00954 #define NIFTI_INTENT_SHAPE        2005
00955 
00956 /* @} */
00957 
00958 /*---------------------------------------------------------------------------*/
00959 /* 3D IMAGE (VOLUME) ORIENTATION AND LOCATION IN SPACE:
00960    ---------------------------------------------------
00961    There are 3 different methods by which continuous coordinates can
00962    attached to voxels.  The discussion below emphasizes 3D volumes, and
00963    the continuous coordinates are referred to as (x,y,z).  The voxel
00964    index coordinates (i.e., the array indexes) are referred to as (i,j,k),
00965    with valid ranges:
00966      i = 0 .. dim[1]-1
00967      j = 0 .. dim[2]-1  (if dim[0] >= 2)
00968      k = 0 .. dim[3]-1  (if dim[0] >= 3)
00969    The (x,y,z) coordinates refer to the CENTER of a voxel.  In methods
00970    2 and 3, the (x,y,z) axes refer to a subject-based coordinate system,
00971    with
00972      +x = Right  +y = Anterior  +z = Superior.
00973    This is a right-handed coordinate system.  However, the exact direction
00974    these axes point with respect to the subject depends on qform_code
00975    (Method 2) and sform_code (Method 3).
00976 
00977    N.B.: The i index varies most rapidly, j index next, k index slowest.
00978     Thus, voxel (i,j,k) is stored starting at location
00979       (i + j*dim[1] + k*dim[1]*dim[2]) * (bitpix/8)
00980     into the dataset array.
00981 
00982    N.B.: The ANALYZE 7.5 coordinate system is
00983       +x = Left  +y = Anterior  +z = Superior
00984     which is a left-handed coordinate system.  This backwardness is
00985     too difficult to tolerate, so this NIFTI-1 standard specifies the
00986     coordinate order which is most common in functional neuroimaging.
00987 
00988    N.B.: The 3 methods below all give the locations of the voxel centers
00989     in the (x,y,z) coordinate system.  In many cases, programs will wish
00990     to display image data on some other grid.  In such a case, the program
00991     will need to convert its desired (x,y,z) values into (i,j,k) values
00992     in order to extract (or interpolate) the image data.  This operation
00993     would be done with the inverse transformation to those described below.
00994 
00995    N.B.: Method 2 uses a factor 'qfac' which is either -1 or 1; qfac is
00996     stored in the otherwise unused pixdim[0].  If pixdim[0]=0.0 (which
00997     should not occur), we take qfac=1.  Of course, pixdim[0] is only used
00998     when reading a NIFTI-1 header, not when reading an ANALYZE 7.5 header.
00999 
01000    N.B.: The units of (x,y,z) can be specified using the xyzt_units field.
01001 
01002    METHOD 1 (the "old" way, used only when qform_code = 0):
01003    -------------------------------------------------------
01004    The coordinate mapping from (i,j,k) to (x,y,z) is the ANALYZE
01005    7.5 way.  This is a simple scaling relationship:
01006 
01007      x = pixdim[1] * i
01008      y = pixdim[2] * j
01009      z = pixdim[3] * k
01010 
01011    No particular spatial orientation is attached to these (x,y,z)
01012    coordinates.  (NIFTI-1 does not have the ANALYZE 7.5 orient field,
01013    which is not general and is often not set properly.)  This method
01014    is not recommended, and is present mainly for compatibility with
01015    ANALYZE 7.5 files.
01016 
01017    METHOD 2 (used when qform_code > 0, which should be the "normal" case):
01018    ---------------------------------------------------------------------
01019    The (x,y,z) coordinates are given by the pixdim[] scales, a rotation
01020    matrix, and a shift.  This method is intended to represent
01021    "scanner-anatomical" coordinates, which are often embedded in the
01022    image header (e.g., DICOM fields (0020,0032), (0020,0037), (0028,0030),
01023    and (0018,0050)), and represent the nominal orientation and location of
01024    the data.  This method can also be used to represent "aligned"
01025    coordinates, which would typically result from some post-acquisition
01026    alignment of the volume to a standard orientation (e.g., the same
01027    subject on another day, or a rigid rotation to true anatomical
01028    orientation from the tilted position of the subject in the scanner).
01029    The formula for (x,y,z) in terms of header parameters and (i,j,k) is:
01030 
01031      [ x ]   [ R11 R12 R13 ] [        pixdim[1] * i ]   [ qoffset_x ]
01032      [ y ] = [ R21 R22 R23 ] [        pixdim[2] * j ] + [ qoffset_y ]
01033      [ z ]   [ R31 R32 R33 ] [ qfac * pixdim[3] * k ]   [ qoffset_z ]
01034 
01035    The qoffset_* shifts are in the NIFTI-1 header.  Note that the center
01036    of the (i,j,k)=(0,0,0) voxel (first value in the dataset array) is
01037    just (x,y,z)=(qoffset_x,qoffset_y,qoffset_z).
01038 
01039    The rotation matrix R is calculated from the quatern_* parameters.
01040    This calculation is described below.
01041 
01042    The scaling factor qfac is either 1 or -1.  The rotation matrix R
01043    defined by the quaternion parameters is "proper" (has determinant 1).
01044    This may not fit the needs of the data; for example, if the image
01045    grid is
01046      i increases from Left-to-Right
01047      j increases from Anterior-to-Posterior
01048      k increases from Inferior-to-Superior
01049    Then (i,j,k) is a left-handed triple.  In this example, if qfac=1,
01050    the R matrix would have to be
01051 
01052      [  1   0   0 ]
01053      [  0  -1   0 ]  which is "improper" (determinant = -1).
01054      [  0   0   1 ]
01055 
01056    If we set qfac=-1, then the R matrix would be
01057 
01058      [  1   0   0 ]
01059      [  0  -1   0 ]  which is proper.
01060      [  0   0  -1 ]
01061 
01062    This R matrix is represented by quaternion [a,b,c,d] = [0,1,0,0]
01063    (which encodes a 180 degree rotation about the x-axis).
01064 
01065    METHOD 3 (used when sform_code > 0):
01066    -----------------------------------
01067    The (x,y,z) coordinates are given by a general affine transformation
01068    of the (i,j,k) indexes:
01069 
01070      x = srow_x[0] * i + srow_x[1] * j + srow_x[2] * k + srow_x[3]
01071      y = srow_y[0] * i + srow_y[1] * j + srow_y[2] * k + srow_y[3]
01072      z = srow_z[0] * i + srow_z[1] * j + srow_z[2] * k + srow_z[3]
01073 
01074    The srow_* vectors are in the NIFTI_1 header.  Note that no use is
01075    made of pixdim[] in this method.
01076 
01077    WHY 3 METHODS?
01078    --------------
01079    Method 1 is provided only for backwards compatibility.  The intention
01080    is that Method 2 (qform_code > 0) represents the nominal voxel locations
01081    as reported by the scanner, or as rotated to some fiducial orientation and
01082    location.  Method 3, if present (sform_code > 0), is to be used to give
01083    the location of the voxels in some standard space.  The sform_code
01084    indicates which standard space is present.  Both methods 2 and 3 can be
01085    present, and be useful in different contexts (method 2 for displaying the
01086    data on its original grid; method 3 for displaying it on a standard grid).
01087 
01088    In this scheme, a dataset would originally be set up so that the
01089    Method 2 coordinates represent what the scanner reported.  Later,
01090    a registration to some standard space can be computed and inserted
01091    in the header.  Image display software can use either transform,
01092    depending on its purposes and needs.
01093 
01094    In Method 2, the origin of coordinates would generally be whatever
01095    the scanner origin is; for example, in MRI, (0,0,0) is the center
01096    of the gradient coil.
01097 
01098    In Method 3, the origin of coordinates would depend on the value
01099    of sform_code; for example, for the Talairach coordinate system,
01100    (0,0,0) corresponds to the Anterior Commissure.
01101 
01102    QUATERNION REPRESENTATION OF ROTATION MATRIX (METHOD 2)
01103    -------------------------------------------------------
01104    The orientation of the (x,y,z) axes relative to the (i,j,k) axes
01105    in 3D space is specified using a unit quaternion [a,b,c,d], where
01106    a*a+b*b+c*c+d*d=1.  The (b,c,d) values are all that is needed, since
01107    we require that a = sqrt(1.0-(b*b+c*c+d*d)) be nonnegative.  The (b,c,d)
01108    values are stored in the (quatern_b,quatern_c,quatern_d) fields.
01109 
01110    The quaternion representation is chosen for its compactness in
01111    representing rotations. The (proper) 3x3 rotation matrix that
01112    corresponds to [a,b,c,d] is
01113 
01114          [ a*a+b*b-c*c-d*d   2*b*c-2*a*d       2*b*d+2*a*c     ]
01115      R = [ 2*b*c+2*a*d       a*a+c*c-b*b-d*d   2*c*d-2*a*b     ]
01116          [ 2*b*d-2*a*c       2*c*d+2*a*b       a*a+d*d-c*c-b*b ]
01117 
01118          [ R11               R12               R13             ]
01119        = [ R21               R22               R23             ]
01120          [ R31               R32               R33             ]
01121 
01122    If (p,q,r) is a unit 3-vector, then rotation of angle h about that
01123    direction is represented by the quaternion
01124 
01125      [a,b,c,d] = [cos(h/2), p*sin(h/2), q*sin(h/2), r*sin(h/2)].
01126 
01127    Requiring a >= 0 is equivalent to requiring -Pi <= h <= Pi.  (Note that
01128    [-a,-b,-c,-d] represents the same rotation as [a,b,c,d]; there are 2
01129    quaternions that can be used to represent a given rotation matrix R.)
01130    To rotate a 3-vector (x,y,z) using quaternions, we compute the
01131    quaternion product
01132 
01133      [0,x',y',z'] = [a,b,c,d] * [0,x,y,z] * [a,-b,-c,-d]
01134 
01135    which is equivalent to the matrix-vector multiply
01136 
01137      [ x' ]     [ x ]
01138      [ y' ] = R [ y ]   (equivalence depends on a*a+b*b+c*c+d*d=1)
01139      [ z' ]     [ z ]
01140 
01141    Multiplication of 2 quaternions is defined by the following:
01142 
01143      [a,b,c,d] = a*1 + b*I + c*J + d*K
01144      where
01145        I*I = J*J = K*K = -1 (I,J,K are square roots of -1)
01146        I*J =  K    J*K =  I    K*I =  J
01147        J*I = -K    K*J = -I    I*K = -J  (not commutative!)
01148      For example
01149        [a,b,0,0] * [0,0,0,1] = [0,0,-b,a]
01150      since this expands to
01151        (a+b*I)*(K) = (a*K+b*I*K) = (a*K-b*J).
01152 
01153    The above formula shows how to go from quaternion (b,c,d) to
01154    rotation matrix and direction cosines.  Conversely, given R,
01155    we can compute the fields for the NIFTI-1 header by
01156 
01157      a = 0.5  * sqrt(1+R11+R22+R33)    (not stored)
01158      b = 0.25 * (R32-R23) / a       => quatern_b
01159      c = 0.25 * (R13-R31) / a       => quatern_c
01160      d = 0.25 * (R21-R12) / a       => quatern_d
01161 
01162    If a=0 (a 180 degree rotation), alternative formulas are needed.
01163    See the nifti1_io.c function mat44_to_quatern() for an implementation
01164    of the various cases in converting R to [a,b,c,d].
01165 
01166    Note that R-transpose (= R-inverse) would lead to the quaternion
01167    [a,-b,-c,-d].
01168 
01169    The choice to specify the qoffset_x (etc.) values in the final
01170    coordinate system is partly to make it easy to convert DICOM images to
01171    this format.  The DICOM attribute "Image Position (Patient)" (0020,0032)
01172    stores the (Xd,Yd,Zd) coordinates of the center of the first voxel.
01173    Here, (Xd,Yd,Zd) refer to DICOM coordinates, and Xd=-x, Yd=-y, Zd=z,
01174    where (x,y,z) refers to the NIFTI coordinate system discussed above.
01175    (i.e., DICOM +Xd is Left, +Yd is Posterior, +Zd is Superior,
01176         whereas +x is Right, +y is Anterior  , +z is Superior. )
01177    Thus, if the (0020,0032) DICOM attribute is extracted into (px,py,pz), then
01178      qoffset_x = -px   qoffset_y = -py   qoffset_z = pz
01179    is a reasonable setting when qform_code=NIFTI_XFORM_SCANNER_ANAT.
01180 
01181    That is, DICOM's coordinate system is 180 degrees rotated about the z-axis
01182    from the neuroscience/NIFTI coordinate system.  To transform between DICOM
01183    and NIFTI, you just have to negate the x- and y-coordinates.
01184 
01185    The DICOM attribute (0020,0037) "Image Orientation (Patient)" gives the
01186    orientation of the x- and y-axes of the image data in terms of 2 3-vectors.
01187    The first vector is a unit vector along the x-axis, and the second is
01188    along the y-axis.  If the (0020,0037) attribute is extracted into the
01189    value (xa,xb,xc,ya,yb,yc), then the first two columns of the R matrix
01190    would be
01191               [ -xa  -ya ]
01192               [ -xb  -yb ]
01193               [  xc   yc ]
01194    The negations are because DICOM's x- and y-axes are reversed relative
01195    to NIFTI's.  The third column of the R matrix gives the direction of
01196    displacement (relative to the subject) along the slice-wise direction.
01197    This orientation is not encoded in the DICOM standard in a simple way;
01198    DICOM is mostly concerned with 2D images.  The third column of R will be
01199    either the cross-product of the first 2 columns or its negative.  It is
01200    possible to infer the sign of the 3rd column by examining the coordinates
01201    in DICOM attribute (0020,0032) "Image Position (Patient)" for successive
01202    slices.  However, this method occasionally fails for reasons that I
01203    (RW Cox) do not understand.
01204 -----------------------------------------------------------------------------*/
01205 
01206    /* [qs]form_code value:  */      /* x,y,z coordinate system refers to:    */
01207    /*-----------------------*/      /*---------------------------------------*/
01208 
01215 #define NIFTI_XFORM_UNKNOWN      0
01216 
01219 #define NIFTI_XFORM_SCANNER_ANAT 1
01220 
01224 #define NIFTI_XFORM_ALIGNED_ANAT 2
01225 
01229 #define NIFTI_XFORM_TALAIRACH    3
01230 
01233 #define NIFTI_XFORM_MNI_152      4
01234 /* @} */
01235 
01236 /*---------------------------------------------------------------------------*/
01237 /* UNITS OF SPATIAL AND TEMPORAL DIMENSIONS:
01238    ----------------------------------------
01239    The codes below can be used in xyzt_units to indicate the units of pixdim.
01240    As noted earlier, dimensions 1,2,3 are for x,y,z; dimension 4 is for
01241    time (t).
01242     - If dim[4]=1 or dim[0] < 4, there is no time axis.
01243     - A single time series (no space) would be specified with
01244       - dim[0] = 4 (for scalar data) or dim[0] = 5 (for vector data)
01245       - dim[1] = dim[2] = dim[3] = 1
01246       - dim[4] = number of time points
01247       - pixdim[4] = time step
01248       - xyzt_units indicates units of pixdim[4]
01249       - dim[5] = number of values stored at each time point
01250 
01251    Bits 0..2 of xyzt_units specify the units of pixdim[1..3]
01252     (e.g., spatial units are values 1..7).
01253    Bits 3..5 of xyzt_units specify the units of pixdim[4]
01254     (e.g., temporal units are multiples of 8).
01255 
01256    This compression of 2 distinct concepts into 1 byte is due to the
01257    limited space available in the 348 byte ANALYZE 7.5 header.  The
01258    macros XYZT_TO_SPACE and XYZT_TO_TIME can be used to mask off the
01259    undesired bits from the xyzt_units fields, leaving "pure" space
01260    and time codes.  Inversely, the macro SPACE_TIME_TO_XYZT can be
01261    used to assemble a space code (0,1,2,...,7) with a time code
01262    (0,8,16,32,...,56) into the combined value for xyzt_units.
01263 
01264    Note that codes are provided to indicate the "time" axis units are
01265    actually frequency in Hertz (_HZ), in part-per-million (_PPM)
01266    or in radians-per-second (_RADS).
01267 
01268    The toffset field can be used to indicate a nonzero start point for
01269    the time axis.  That is, time point #m is at t=toffset+m*pixdim[4]
01270    for m=0..dim[4]-1.
01271 -----------------------------------------------------------------------------*/
01272 
01279 #define NIFTI_UNITS_UNKNOWN 0
01280 
01283 #define NIFTI_UNITS_METER   1
01284 
01285 #define NIFTI_UNITS_MM      2
01286 
01287 #define NIFTI_UNITS_MICRON  3
01288 
01291 #define NIFTI_UNITS_SEC     8
01292 
01293 #define NIFTI_UNITS_MSEC   16
01294 
01295 #define NIFTI_UNITS_USEC   24
01296 
01297                                /*** These units are for spectral data: ***/
01299 #define NIFTI_UNITS_HZ     32
01300 
01301 #define NIFTI_UNITS_PPM    40
01302 
01303 #define NIFTI_UNITS_RADS   48
01304 /* @} */
01305 
01306 #undef  XYZT_TO_SPACE
01307 #undef  XYZT_TO_TIME
01308 #define XYZT_TO_SPACE(xyzt)       ( (xyzt) & 0x07 )
01309 #define XYZT_TO_TIME(xyzt)        ( (xyzt) & 0x38 )
01310 
01311 #undef  SPACE_TIME_TO_XYZT
01312 #define SPACE_TIME_TO_XYZT(ss,tt) (  (((char)(ss)) & 0x07)   \
01313                                    | (((char)(tt)) & 0x38) )
01314 
01315 /*---------------------------------------------------------------------------*/
01316 /* MRI-SPECIFIC SPATIAL AND TEMPORAL INFORMATION:
01317    ---------------------------------------------
01318    A few fields are provided to store some extra information
01319    that is sometimes important when storing the image data
01320    from an FMRI time series experiment.  (After processing such
01321    data into statistical images, these fields are not likely
01322    to be useful.)
01323 
01324   { freq_dim  } = These fields encode which spatial dimension (1,2, or 3)
01325   { phase_dim } = corresponds to which acquisition dimension for MRI data.
01326   { slice_dim } =
01327     Examples:
01328       Rectangular scan multi-slice EPI:
01329         freq_dim = 1  phase_dim = 2  slice_dim = 3  (or some permutation)
01330       Spiral scan multi-slice EPI:
01331         freq_dim = phase_dim = 0  slice_dim = 3
01332         since the concepts of frequency- and phase-encoding directions
01333         don't apply to spiral scan
01334 
01335     slice_duration = If this is positive, AND if slice_dim is nonzero,
01336                      indicates the amount of time used to acquire 1 slice.
01337                      slice_duration*dim[slice_dim] can be less than pixdim[4]
01338                      with a clustered acquisition method, for example.
01339 
01340     slice_code = If this is nonzero, AND if slice_dim is nonzero, AND
01341                  if slice_duration is positive, indicates the timing
01342                  pattern of the slice acquisition.  The following codes
01343                  are defined:
01344                    NIFTI_SLICE_SEQ_INC  == sequential increasing
01345                    NIFTI_SLICE_SEQ_DEC  == sequential decreasing
01346                    NIFTI_SLICE_ALT_INC  == alternating increasing
01347                    NIFTI_SLICE_ALT_DEC  == alternating decreasing
01348                    NIFTI_SLICE_ALT_INC2 == alternating increasing #2
01349                    NIFTI_SLICE_ALT_DEC2 == alternating decreasing #2
01350   { slice_start } = Indicates the start and end of the slice acquisition
01351   { slice_end   } = pattern, when slice_code is nonzero.  These values
01352                     are present to allow for the possible addition of
01353                     "padded" slices at either end of the volume, which
01354                     don't fit into the slice timing pattern.  If there
01355                     are no padding slices, then slice_start=0 and
01356                     slice_end=dim[slice_dim]-1 are the correct values.
01357                     For these values to be meaningful, slice_start must
01358                     be non-negative and slice_end must be greater than
01359                     slice_start.  Otherwise, they should be ignored.
01360 
01361   The following table indicates the slice timing pattern, relative to
01362   time=0 for the first slice acquired, for some sample cases.  Here,
01363   dim[slice_dim]=7 (there are 7 slices, labeled 0..6), slice_duration=0.1,
01364   and slice_start=1, slice_end=5 (1 padded slice on each end).
01365 
01366   slice
01367   index  SEQ_INC SEQ_DEC ALT_INC ALT_DEC ALT_INC2 ALT_DEC2
01368     6  :   n/a     n/a     n/a     n/a    n/a      n/a    n/a = not applicable
01369     5  :   0.4     0.0     0.2     0.0    0.4      0.2    (slice time offset
01370     4  :   0.3     0.1     0.4     0.3    0.1      0.0     doesn't apply to
01371     3  :   0.2     0.2     0.1     0.1    0.3      0.3     slices outside
01372     2  :   0.1     0.3     0.3     0.4    0.0      0.1     the range
01373     1  :   0.0     0.4     0.0     0.2    0.2      0.4     slice_start ..
01374     0  :   n/a     n/a     n/a     n/a    n/a      n/a     slice_end)
01375 
01376   The SEQ slice_codes are sequential ordering (uncommon but not unknown),
01377   either increasing in slice number or decreasing (INC or DEC), as
01378   illustrated above.
01379 
01380   The ALT slice codes are alternating ordering.  The 'standard' way for
01381   these to operate (without the '2' on the end) is for the slice timing
01382   to start at the edge of the slice_start .. slice_end group (at slice_start
01383   for INC and at slice_end for DEC).  For the 'ALT_*2' slice_codes, the
01384   slice timing instead starts at the first slice in from the edge (at
01385   slice_start+1 for INC2 and at slice_end-1 for DEC2).  This latter
01386   acquisition scheme is found on some Siemens scanners.
01387 
01388   The fields freq_dim, phase_dim, slice_dim are all squished into the single
01389   byte field dim_info (2 bits each, since the values for each field are
01390   limited to the range 0..3).  This unpleasantness is due to lack of space
01391   in the 348 byte allowance.
01392 
01393   The macros DIM_INFO_TO_FREQ_DIM, DIM_INFO_TO_PHASE_DIM, and
01394   DIM_INFO_TO_SLICE_DIM can be used to extract these values from the
01395   dim_info byte.
01396 
01397   The macro FPS_INTO_DIM_INFO can be used to put these 3 values
01398   into the dim_info byte.
01399 -----------------------------------------------------------------------------*/
01400 
01401 #undef  DIM_INFO_TO_FREQ_DIM
01402 #undef  DIM_INFO_TO_PHASE_DIM
01403 #undef  DIM_INFO_TO_SLICE_DIM
01404 
01405 #define DIM_INFO_TO_FREQ_DIM(di)   ( ((di)     ) & 0x03 )
01406 #define DIM_INFO_TO_PHASE_DIM(di)  ( ((di) >> 2) & 0x03 )
01407 #define DIM_INFO_TO_SLICE_DIM(di)  ( ((di) >> 4) & 0x03 )
01408 
01409 #undef  FPS_INTO_DIM_INFO
01410 #define FPS_INTO_DIM_INFO(fd,pd,sd) ( ( ( ((char)(fd)) & 0x03)      ) |  \
01411                                       ( ( ((char)(pd)) & 0x03) << 2 ) |  \
01412                                       ( ( ((char)(sd)) & 0x03) << 4 )  )
01413 
01419 #define NIFTI_SLICE_UNKNOWN   0
01420 #define NIFTI_SLICE_SEQ_INC   1
01421 #define NIFTI_SLICE_SEQ_DEC   2
01422 #define NIFTI_SLICE_ALT_INC   3
01423 #define NIFTI_SLICE_ALT_DEC   4
01424 #define NIFTI_SLICE_ALT_INC2  5  /* 05 May 2005: RWCox */
01425 #define NIFTI_SLICE_ALT_DEC2  6  /* 05 May 2005: RWCox */
01426 /* @} */
01427 
01428 /*---------------------------------------------------------------------------*/
01429 /* UNUSED FIELDS:
01430    -------------
01431    Some of the ANALYZE 7.5 fields marked as ++UNUSED++ may need to be set
01432    to particular values for compatibility with other programs.  The issue
01433    of interoperability of ANALYZE 7.5 files is a murky one -- not all
01434    programs require exactly the same set of fields.  (Unobscuring this
01435    murkiness is a principal motivation behind NIFTI-1.)
01436 
01437    Some of the fields that may need to be set for other (non-NIFTI aware)
01438    software to be happy are:
01439 
01440      extents    dbh.h says this should be 16384
01441      regular    dbh.h says this should be the character 'r'
01442      glmin,   } dbh.h says these values should be the min and max voxel
01443       glmax   }  values for the entire dataset
01444 
01445    It is best to initialize ALL fields in the NIFTI-1 header to 0
01446    (e.g., with calloc()), then fill in what is needed.
01447 -----------------------------------------------------------------------------*/
01448 
01449 /*---------------------------------------------------------------------------*/
01450 /* MISCELLANEOUS C MACROS
01451 -----------------------------------------------------------------------------*/
01452 
01453 /*.................*/
01457 #define NIFTI_VERSION(h)                               \
01458  ( ( (h).magic[0]=='n' && (h).magic[3]=='\0'    &&     \
01459      ( (h).magic[1]=='i' || (h).magic[1]=='+' ) &&     \
01460      ( (h).magic[2]>='1' && (h).magic[2]<='9' )   )    \
01461  ? (h).magic[2]-'0' : 0 )
01462 
01463 /*.................*/
01468 #define NIFTI_ONEFILE(h) ( (h).magic[1] == '+' )
01469 
01470 /*.................*/
01474 #define NIFTI_NEEDS_SWAP(h) ( (h).dim[0] < 0 || (h).dim[0] > 7 )
01475 
01476 /*.................*/
01480 #define NIFTI_5TH_DIM(h) ( ((h).dim[0]>4 && (h).dim[5]>1) ? (h).dim[5] : 0 )
01481 
01482 /*****************************************************************************/
01483 
01484 /*=================*/
01485 #ifdef  __cplusplus
01486 }
01487 #endif
01488 /*=================*/
01489 
01490 #endif /* _NIFTI_HEADER_ */

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