AnalyzeFMRI (version 1.1-25)

analyze2nifti: Create a NIFTI file from an Analyze file

Description

Create a NIFTI file from an Analyze file.

Usage

analyze2nifti(file.in,path.in=".",path.out=NULL,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)))

Value

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

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.

Examples

tmpdir <- tempdir()
analyze2nifti(path.in = system.file(package = "AnalyzeFMRI"),
              path.out = tmpdir, file.in = "example",
              file.out = "nifti-tmp", is.nii = TRUE)
unlink(tmpdir) # tidy up