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.