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.