| analyze2nifti {AnalyzeFMRI} | R Documentation |
Create a NIFTI file from an Analyze file.
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)))
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 |
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 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. |
Nothing is returned. The NIFTI file is created in the specified path.out directory (default is current directory).
analyze2nifti(path.in=system.file(package="AnalyzeFMRI"),file.in="example",file.out="nifti-tmp",is.nii=TRUE)