f.read.nifti.header {AnalyzeFMRI}R Documentation

read Nifti header file

Description

Reads the NIFTI image format .hdr (or .nii) header file into a list.

Usage

f.read.nifti.header(file)

Arguments

file

The .hdr (or .nii) file to be read

Value

A list containing the information in the fields of the .hdr (.nii) file.

file.name

path name of the .img file

swap

1 or 0 variable indicating whether files are big (=native) or little (=swapped) endian

sizeof.hdr

MUST be 348

data.type

char[10]. UNUSED

db.name

char[18]. UNUSED

extents

UNUSED

session.error

UNUSED

regular

UNUSED, but filled with 'r' as SPM does

dim.info

MRI slice ordering: This field encode which spatial dimension (1=x, 2=y, or 3=z) corresponds to which acquisition dimension for MRI data. In fact, it contains three informations: freq.dim, phase.dim and slice.dim, all squished into the single byte field dim.info (2 bits each, since the values for each field are limited to the range 0..3). The R function diminfo2fps can be used to extract these values from the dim.info byte.

dim

vector (of length 8) of image dimensions. dim[1] specifies the number of dimensions. In NIFTI-1 files, dim[2], dim[3], dim[4] are for space, dim[5] is for time. The 5th dimension (dim[6]) of the dataset, if present (i.e., dim[1]=5 and dim[6] > 1), contains multiple values (for example a vector) to be stored at each spatiotemporal location. Uses of dim[7] and dim[8] are not specified in NIFTI-1 format.

intent.p1

1st intent parameter: first auxiliary parameter for a possible statistical distribution specified in intent.code

intent.p2

2nd intent parameter: second auxiliary parameter for a possible statistical distribution specified in intent.code

intent.p3

3rd intent parameter: third auxiliary parameter for a possible statistical distribution specified in intent.code

intent.code

NIFTI INTENT code: if 0, this is a raw dataset; if in range 2...24, this indicates that the numbers in the dataset should be interpreted as being drawn from a given distribution. Most such distributions have auxiliary parameters (given with intent.p?); if in range 1001...1011, this is an other meaning. See file intent-code.txt in the niftidoc directory of the source package. If the dataset DOES NOT have a 5th dimension (dim[1]=4), 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 (dim[1]=5), then the auxiliary parameters are different for each voxel.

datatype

integer indicator of data storage type for each voxel. This could be 0 (unknown), 2 (unsigned char = 1 byte), 4 (signed short = 2 bytes), 8 (signed int = 4 bytes), 16 (32 bit float = 4 bytes), 32 (64 bit complex = two 32 bit floats = 8 bytes), 64 (64 bits float = double = 8 bytes), 128 (RGB triple = three 8 bits bytes = 3 bytes), 256 (signed char = 1 byte), 512 (unsigned short = 2 bytes), 768 (unsigned int = 4 bytes), 1024 (signed long long = 8 bytes), 1280 (unsigned long long = 8 bytes), 1536 (128 bit float = long double = 16 bytes), 1792 (128 bit complex = 2 64 bit floats = 16 bytes), 2048 (256 bit complex = 2 128 bit floats = 32 bytes).

bitpix

the number of bits per voxel. This field MUST correspond with the datatype field. The total number of bytes in the image data is dim[2]* ... * dim[dim[1]+1] * bitpix / 8

slice.start

Indicates the start of the slice acquisition pattern, when slice.code is nonzero. These values are present to allow for the possible addition of "padded" slices at either end of the volume, which don't fit into the slice timing pattern. If there are no padding slices, then slice.start=0 and slice.end=dim[slice.dim+1]-1 are the correct values. For these values to be meaningful, slice.start must be non-negative and slice.end must be greater than slice.start.

pixdim

vector (of length 8). Grid spacings. When reading a NIFTI-1 header, pixdim[1] stores qfac (which is either -1 or 1). If pixdim[1]=0 (which should not occur), we take qfac=1. pixdim[2], pixdim[3] and pixdim[4] give the voxel width along dimension x, y and z respectively. pixdim[5] gives the time step (=Time Repetition=TR). The units of pixdim can be specified with the xyzt.units field.

vox.offset

Offset into .nii file. Should be 352 for a .nii file, 0 for a nifti .hdr/.img pair.

scl.slope

Data scaling: If the scl.slope field is nonzero, then each voxel value in the dataset should be scaled as y = scl.slope*x + scl.inter, where x = voxel value stored and y = "true" voxel value

scl.inter

Data scaling: offset. Idem above.

slice.end

Indicates the end of the slice acquisition pattern, when slice.code is nonzero. These values are present to allow for the possible addition of "padded" slices at either end of the volume, which don't fit into the slice timing pattern. If there are no padding slices, then slice.start=0 and slice.end=dim[slice.dim+1]-1 are the correct values. For these values to be meaningful, slice.start must be non-negative and slice.end must be greater than slice.start.

slice.code

Slice timing order. If this is nonzero, AND if slice.dim is nonzero, AND if slice.duration is positive, indicates the timing pattern of the slice acquisition. The following codes are defined: 0 (unknown), 1 (sequential increasing), 2 (sequential decreasing), 3 (alternating increasing), 4 (alternating decreasing), 5 (alternating increasing #2), 6 (alternating decreasing #2)

xyzt.units

Units of pixdim[2:5]. Bits 1..3 of xyzt.units specify the (same) space unit of pixdim[2:4]. Bits 4..6 of xyzt.units specify the time unit of pixdim[5]. See xyzt-units.txt in the niftidoc directory of the source package. The R function xyzt2st can be used to extract these values from the xyzt.units byte.

cal.max

Maximum display intensity (white) corresponds to dataset value cal.max. Dataset values above cal.max should display as white. cal.min and cal.max only make sense when applied to scalar-valued datasets (i.e., dim[1] < 5 or dim[6] = 1).

cal.min

Minimum display intensity (black) corresponds to dataset value cal.min. Dataset values below cal.min should display as black.

slice.duration

Time for 1 slice. If this is positive, AND if slice.dim is nonzero, indicates the amount of time used to acquire 1 slice.

toffset

Time axis shift: The toffset field can be used to indicate a nonzero start point for the time axis. That is, time point m is at t=toffset+m*pixdim[5] for m=1, ..., dim[5]-1.

glmax

UNUSED

glmin

UNUSED

descrip

char[80]. This field may contain any text you like

aux.file

char[24]. This field is used to store an auxiliary filename.

qform.code

NIFTI code (in 0, ... ,4). 0: Arbitrary coordinates; 1: Scanner-based anatomical coordinates; 2: Coordinates aligned to another file's, or to anatomical "truth" (coregistration); 3: Coordinates aligned to Talairach-Tournoux Atlas; 4: MNI 152 normalized coordinates

sform.code

NIFTI code (in 0, ... ,4) with the same meaning as qform codes. The basic idea behind having two coordinate systems is to allow the image to store information about (1) the scanner coordinate system used in the acquisition of the volume (in the qform) and (2) the relationship to a standard coordinate system - e.g. MNI coordinates (in the sform). The qform allows orientation information to be kept for alignment purposes without losing volumetric information, since the qform only stores a rigid-body transformation (rotation and translation) which preserves volume. On the other hand, the sform stores a general affine transformation (shear, scale, rotation and translation) which can map the image coordinates into a standard coordinate system, like Talairach or MNI, without the need to resample the image. By having both coordinate systems, it is possible to keep the original data (without resampling), along with information on how it was acquired (qform) and how it relates to other images via a standard space (sform). This ability is advantageous for many analysis pipelines, and has previously required storing additional files along with the image files. By using NIfTI-1 this extra information can be kept in the image files themselves. Note: the qform and sform also store information on whether the coordinate system is left-handed or right-handed and so when both are set they must be consistent, otherwise the handedness of the coordinate system (often used to distinguish left-right order) is unknown and the results of applying operations to such an image are unspecified.

quatern.b

Quaternion b param. These b,c,d quaternion parameters encode a rotation matrix used when qform.code > 0 to obtain a rigid transformation that maps voxel indices (i,j,k) to spatial coordinates (x,y,z), typically anatomical coordinates assigned by the scanner. This transformation ("Method 2" in the nifti1.h documentation) is generated using also the voxel dimensions (pixdim[1:4]) and a 3D shift, i.e. a translation, (qoffset.*)

quatern.c

Quaternion c param

quatern.d

Quaternion d param

qoffset.x

Quaternion x shift. If the (0020,0032) DICOM attribute is extracted into (px,py,pz), then qoffset.x = -px qoffset.y = -py qoffset.z = pz is a reasonable setting when qform.code=NIFTI XFORM SCANNER ANAT.

qoffset.y

Quaternion y shift

qoffset.z

Quaternion z shift

srow.x

vector of length 4. 1st row affine transform. These srow.* parameters contain an affine (non-rigid) transformation ("Method 3" in the nifti1.h documentation) that maps voxel indices (i,j,k) to spatial coordinates (x,y,z).

srow.y

vector of length 4. 2nd row affine transform

srow.z

vector of length 4. 3rd row affine transform

intent.name

char[16]. 'name' or meaning of data. If no data name is implied or needed, intent.name[1] should be set to 0.

magic

MUST be "nix" or "n+x", where x in 0...9

extension

By default,all 4 bytes of this array should be set to zero. In a .nii file, these 4 bytes will always be present, since the earliest start point for the image data is byte #352. In a separate .hdr file, these bytes may or may not be present. If not present (i.e., if the length of the .hdr file is 348 bytes), then a NIfTI-1 compliant program should use the default value of extension=0,0,0,0. The first byte (extension[0]) is the only value of this array that is specified at present. The other 3 bytes are reserved for future use.

If extension[0] is nonzero, it indicates that extended header information is present in the bytes following the extension array. In a .nii file, this extended header data is before the image data (and vox_offset must be set correctly to allow for this). In a .hdr file, this extended data follows extension and proceeds (potentially) to the end of the file.

Examples

f.read.nifti.header(system.file("example-nifti.hdr", package="AnalyzeFMRI"))

[Package AnalyzeFMRI version 1.1-24 Index]