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
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
qform.code value (in 0,...4)
sform.code
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 f
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), c
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 SLI
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
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.