analyze2nifti: Create a NIFTI file from an Analyze file

In AnalyzeFMRI: Functions for Analysis of fMRI Datasets Stored in the ANALYZE or NIFTI Format

Description

Create a NIFTI file from an Analyze file.

Usage

analyze2nifti(file.in,path.in=".",path.out=".",file.out=NULL,is.nii=TRUE,
qform.code=2,sform.code=2,data.type=rawToChar(raw(10)),db.name=rawToChar(raw(18)),
dim.info=rawToChar(raw(1)),dim=NULL,TR=0,slice.code=rawToChar(raw(1)),
xyzt.units=rawToChar(raw(1)),descrip=NULL,aux.file=rawToChar(raw(24)),
intent.name=rawToChar(raw(16)))

Arguments

file.in	character, filename of the Analyze file to be read
path.in	character, Directory path from where to take the .hdr,.img,.mat files
path.out	character, Directory path where to write the .hdr/.img or .nii file
file.out	character, filename of the NIFTI file to write (without extension). If NULL, same as file.in
is.nii	logical, if TRUE a NIFTI .nii file will be created, if FALSE a .hdr/.img NIFTI file will be created
qform.code	value in 0,...,4
sform.code	value in 0,...,4
data.type	char[10]. UNUSED in NIFTI-1 but could be filled with what you want
db.name	char[18]. UNUSED in NIFTI-1 but could be filled with what you want
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 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.
TR	Time Repetition to be stored in pixdim[5]
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 from the xyzt.units byte.
descrip	char[80]. This field may contain any text you like
aux.file	char[24]. This field is used to store an auxiliary filename.
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

Nothing is returned. The NIFTI file is created in the specified path.out directory (default is current directory).

Examples

## Not run: 
analyze2nifti(path.in=system.file(package="AnalyzeFMRI"),file.in="example",
              file.out="nifti-tmp",is.nii=TRUE)

## End(Not run)

Example output

Loading required package: R.matlab
R.matlab v3.6.2 (2018-09-26) successfully loaded. See ?R.matlab for help.

Attaching package: 'R.matlab'

The following objects are masked from 'package:base':

    getOption, isOpen

Loading required package: fastICA
Loading required package: tcltk
Loading required package: tkrplot
Warning messages:
1: no DISPLAY variable so Tk is not available 
2: loading Rplot failed 

AnalyzeFMRI documentation built on Oct. 5, 2021, 5:06 p.m.