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.

parrec2nii 5.2.1                                  February 2024                                    PARREC2NII(1)