f.complete.hdr.nifti.list.create {AnalyzeFMRI}R Documentation

creates complete .hdr list in NIFTI format

Description

Creates a complete list that can be used to write a .hdr file or the header part of a .nii file

Usage

f.complete.hdr.nifti.list.create(file,dim.info=character(1),dim,
intent.p1=single(1),intent.p2=single(1),intent.p3=single(1),intent.code=integer(1),
datatype=integer(1),bitpix=integer(1),slice.start=integer(1),pixdim=single(8),
scl.slope=single(1),scl.inter=single(1),slice.end=integer(1),slice.code=character(1),
xyzt.units=character(1),cal.max=single(1),cal.min=single(1),slice.duration=single(1),
toffset=single(1),descrip=paste(rep(" ", 80), sep = "", collapse = ""),
aux.file=paste(rep(" ", 24), sep = "", collapse =""),qform.code=integer(1),
sform.code=integer(1),quatern.b=single(1),quatern.c=single(1),quatern.d=single(1),
qoffset.x=single(1),qoffset.y=single(1),qoffset.z=single(1),srow.x=single(4),
srow.y=single(4),srow.z=single(4),
intent.name=paste(rep(" ", 16), sep = "", collapse = ""))

Arguments

file

The .hdr filename. If file extension is ".nii", this will create a header file for a ".nii" NIFTI file, else for a .hdr/.img NIFTI pair

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 fps2diminfo can be used to encode these values into the dim.info character 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 spatio-temporal 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 2 (unsigned char), 4 (signed short), 8 (signed int), 16 (32 bit float), 32 (64 bit complex = two 32 bit floats), 64 (64 bit float = double), 128 (3 8 bit bytes), 256 (signed char), 512 (unsigned short), 768 (unsigned int), 1024 (signed long long), 1280 (unsigned long long), 1536 (128 bit float = long double), 1792 (128 bit complex = 2 64 bit floats), 2048 (256 bit complex = 2 128 bit floats).

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.

scl.slope

Data scaling: If the scl.slope field is nonzero, then each voxel value in the dataset should be scaled as y = \code{scl.slope}*x + \code{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 (NIFTI SLICE UNKNOWN), 1 (NIFTI SLICE SEQ INC), 2 (NIFTI SLICE SEQ DEC), 3 (NIFTI SLICE ALT INC), 4 (NIFTI SLICE ALT DEC)

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 st2xyzt can be used to encode these values into 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=\code{toffset}+m*\code{pixdim[5]} for m=1, ..., dim[5]-1.

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 and 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.

Value

Returns a list of all the fields needed to create a .hdr file (see the function code for details).

See Also

f.basic.hdr.nifti.list.create, f.write.list.to.hdr.nifti, f.nifti.file.summary

Examples

## Not run: 
dim.mat <- c(20,30,40,3)
dim <- c(length(dim.mat), dim.mat, rep(0, 7 - length(dim.mat)))
filename <- "temp.hdr"
f.complete.hdr.nifti.list.create(file=filename,dim=dim)

## End(Not run)

[Package AnalyzeFMRI version 1.1-23 Index]