parrec2nii - convert PARREC image to NIfTI
parrec2nii [OPTIONS] <PAR files>
Code for PAR/REC to NIfTI converter command
- --version
- show program's version number and exit
- -h, --help
- show this help message and exit
- -v, --verbose
- Make some noise.
- -o OUTDIR,
--output-dir=OUTDIR
- Destination directory for NIfTI files. Default: current directory.
- -c,
--compressed
- Whether to write compressed NIfTI files or not.
- -p,
--permit-truncated
- Permit conversion of truncated recordings. Support for this is
experimental, and results *must* be checked afterward for validity.
- -b, --bvs
- Output bvals/bvecs files in addition to NIFTI image.
- -d,
--dwell-time
- Calculate the scan dwell time. If supplied, the magnetic field strength
should also be supplied using --field-strength (default 3). The
field strength must be supplied because it is not encoded in the PAR/REC
format.
- --field-strength=FIELD_STRENGTH
- The magnetic field strength of the recording, only needed for
--dwell-time. The field strength must be supplied because it is not
encoded in the PAR/REC format.
- -i,
--volume-info
- Export .PAR volume labels corresponding to the fourth dimension of the
data. The dimension info will be stored in CSV format with the first row
containing dimension labels and the subsequent rows (one per volume), the
corresponding indices. Only labels that vary along the 4th dimension are
exported (e.g. for a single volume structural scan there are no dynamic
labels and no output file will be created).
- --origin=ORIGIN
- Reference point of the q-form transformation of the NIfTI image. If
'scanner' the (0,0,0) coordinates will refer to the scanner's iso center.
If 'fov', this coordinate will be the center of the recorded volume (field
of view). Default: 'scanner'.
- --minmax=MINMAX
- Minimum and maximum settings to be stored in the NIfTI header. If any of
them is set to 'parse', the scaled data is scanned for the actual minimum
and maximum. To bypass this potentially slow and memory intensive step
(the data has to be scaled and fully loaded into memory), fixed values can
be provided as spaceseparated pair, e.g. '5.4 120.4'. It is possible to
set a fixed minimum as scan for the actual maximum (and vice versa).
Default: 'parse parse'.
- --store-header
- If set, all information from the PAR header is stored in an extension of
the NIfTI file header. Default: off
- --scaling=SCALING
- Choose data scaling setting. The PAR header defines two different data
scaling settings: 'dv' (values displayed on console) and 'fp' (floating
point values). Either one can be chosen, or scaling can be disabled
completely ('off'). Note that neither method will actually scale the data,
but just store the corresponding settings in the NIfTI header, unless
non-uniform scaling is used, in which case the data is stored in the file
in scaled form. Default: 'dv'
- --keep-trace
- Do not discard the diagnostic Philips DTI trace volume, if it exists in
the data.
- --overwrite
- Overwrite file if it exists. Default: False
- --strict-sort
- Use additional keys in determining the order to sort the slices within the
.REC file. This may be necessary for more complicated scans with multiple
echos, cardiac phases, ASL label states, etc.