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nifti1.h header documentation
/---------------------------------------------------------------------------/ /* DATA DIMENSIONALITY (as in ANALYZE 7.5): --------------------------------------- dim[0] = number of dimensions; - if dim[0] is outside range 1..7, then the header information needs to be byte swapped appropriately - ANALYZE supports dim[0] up to 7, but NIFTI-1 reserves dimensions 1,2,3 for space (x,y,z), 4 for time (t), and 5,6,7 for anything else needed.
dim[i] = length of dimension #i, for i=1..dim[0] (must be positive) - also see the discussion of intent_code, far below
pixdim[i] = voxel width along dimension #i, i=1..dim[0] (positive) - cf. ORIENTATION section below for use of pixdim[0] - the units of pixdim can be specified with the xyzt_units field (also described far below).
Number of bits per voxel value is in bitpix, which MUST correspond with the datatype field. The total number of bytes in the image data is dim[1] ... dim[dim[0]] * bitpix / 8
In NIFTI-1 files, dimensions 1,2,3 are for space, dimension 4 is for time, and dimension 5 is for storing multiple values at each spatiotemporal voxel. Some examples: - A typical whole-brain FMRI experiment's time series: - dim[0] = 4 - dim[1] = 64 pixdim[1] = 3.75 xyzt_units = NIFTI_UNITS_MM - dim[2] = 64 pixdim[2] = 3.75 | NIFTI_UNITS_SEC - dim[3] = 20 pixdim[3] = 5.0 - dim[4] = 120 pixdim[4] = 2.0 - A typical T1-weighted anatomical volume: - dim[0] = 3 - dim[1] = 256 pixdim[1] = 1.0 xyzt_units = NIFTI_UNITS_MM - dim[2] = 256 pixdim[2] = 1.0 - dim[3] = 128 pixdim[3] = 1.1 - A single slice EPI time series: - dim[0] = 4 - dim[1] = 64 pixdim[1] = 3.75 xyzt_units = NIFTI_UNITS_MM - dim[2] = 64 pixdim[2] = 3.75 | NIFTI_UNITS_SEC - dim[3] = 1 pixdim[3] = 5.0 - dim[4] = 1200 pixdim[4] = 0.2 - A 3-vector stored at each point in a 3D volume: - dim[0] = 5 - dim[1] = 256 pixdim[1] = 1.0 xyzt_units = NIFTI_UNITS_MM - dim[2] = 256 pixdim[2] = 1.0 - dim[3] = 128 pixdim[3] = 1.1 - dim[4] = 1 pixdim[4] = 0.0 - dim[5] = 3 intent_code = NIFTI_INTENT_VECTOR - A single time series with a 3x3 matrix at each point: - dim[0] = 5 - dim[1] = 1 xyzt_units = NIFTI_UNITS_SEC - dim[2] = 1 - dim[3] = 1 - dim[4] = 1200 pixdim[4] = 0.2 - dim[5] = 9 intent_code = NIFTI_INTENT_GENMATRIX - intent_p1 = intent_p2 = 3.0 (indicates matrix dimensions)
BYTE ORDERING: ------------- The byte order of the data arrays is presumed to be the same as the byte order of the header (which is determined by examining dim[0]).
VECTOR-VALUED DATASETS: ---------------------- The 5th dimension of the dataset, if present (i.e., dim[0]=5 and dim[5] > 1), contains multiple values (e.g., a vector) to be stored at each spatiotemporal location. For example, the header values - dim[0] = 5 - dim[1] = 64 - dim[2] = 64 - dim[3] = 20 - dim[4] = 1 (indicates no time axis) - dim[5] = 3 - datatype = DT_FLOAT - intent_code = NIFTI_INTENT_VECTOR mean that this dataset should be interpreted as a 3D volume (64x64x20), with a 3-vector of floats defined at each point in the 3D grid.
A program reading a dataset with a 5th dimension may want to reformat the image data to store each voxels' set of values together in a struct or array. This programming detail, however, is beyond the scope of the NIFTI-1 file specification! Uses of dimensions 6 and 7 are also not specified here.
STATISTICAL PARAMETRIC DATASETS (i.e., SPMs): -------------------------------------------- Values of intent_code from NIFTI_FIRST_STATCODE to NIFTI_LAST_STATCODE (inclusive) indicate that the numbers in the dataset should be interpreted as being drawn from a given distribution. Most such distributions have auxiliary parameters (e.g., NIFTI_INTENT_TTEST has 1 DOF parameter).
If the dataset DOES NOT have a 5th dimension, then the auxiliary parameters are the same for each voxel, and are given in header fields intent_p1, intent_p2, and intent_p3.
If the dataset DOES have a 5th dimension, then the auxiliary parameters are different for each voxel. For example, the header values - dim[0] = 5 - dim[1] = 128 - dim[2] = 128 - dim[3] = 1 (indicates a single slice) - dim[4] = 1 (indicates no time axis) - dim[5] = 2 - datatype = DT_FLOAT - intent_code = NIFTI_INTENT_TTEST mean that this is a 2D dataset (128x128) of t-statistics, with the t-statistic being in the first "plane" of data and the degrees-of-freedom parameter being in the second "plane" of data.
If the dataset 5th dimension is used to store the voxel-wise statistical parameters, then dim[5] must be 1 plus the number of parameters required by that distribution (e.g., intent_code=NIFTI_INTENT_TTEST implies dim[5] must be 2, as in the example just above).
/---------------------------------------------------------------------------/ /* UNITS OF SPATIAL AND TEMPORAL DIMENSIONS: ---------------------------------------- The codes below can be used in xyzt_units to indicate the units of pixdim. As noted earlier, dimensions 1,2,3 are for x,y,z; dimension 4 is for time (t). - If dim[4]=1 or dim[0] < 4, there is no time axis. - A single time series (no space) would be specified with - dim[0] = 4 (for scalar data) or dim[0] = 5 (for vector data) - dim[1] = dim[2] = dim[3] = 1 - dim[4] = number of time points - pixdim[4] = time step - xyzt_units indicates units of pixdim[4] - dim[5] = number of values stored at each time point
Bits 0..2 of xyzt_units specify the units of pixdim[1..3] (e.g., spatial units are values 1..7). Bits 3..5 of xyzt_units specify the units of pixdim[4] (e.g., temporal units are multiples of 8).
MISCELLANEOUS C MACROS
/! Check if a nifti_1_header struct needs to be byte swapped. Returns 1 if it needs to be swapped, 0 if it does not. /
#define NIFTI_NEEDS_SWAP(h) ( (h).dim[0] < 0 || (h).dim[0] > 7 )
/! Check if a nifti_1_header struct contains a 5th (vector) dimension. Returns size of 5th dimension if > 1, returns 0 otherwise. /
#define NIFTI_5TH_DIM(h) ( ((h).dim[0]>4 && (h).dim[5]>1) ? (h).dim[5] : 0 )
