NAME¶

parrec2nii - convert PARREC image to NIfTI

SYNOPSIS¶

parrec2nii [OPTIONS] <PAR files>

DESCRIPTION¶

Code for PAR/REC to NIfTI converter command

OPTIONS¶

--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.