NAME

       dcm2niix - DICOM to NifTI converter

SYNOPSIS

       dcm2niix [options] <sourcedir>

DESCRIPTION

       Most  medical  imaging  devices save images in some variation of the popular DICOM format.
       However, most scientific tools expect medical images to be  stored  in  the  comparatively
       simpler  NIfTI format. dcm2niix is designed to perform such conversion from DICOM to NIfTI
       with a simple command-line interface.

       Please be advised that dcm2niix has been developed for research purposes only  and  should
       not be considered a clinical tool.

OPTIONS

       -1..-9          gz compression level (1=fastest..9=smallest, default 6)

       -b <y/i/n>
              Save  additional  BIDS  metadata to a side-car .json file.  The "i"nput-only option
              reads DICOMs but saves neither BIDS nor NIfTI.

       -ba <y/n>       anonymize BIDS

       -f <format>
              Format string for the output filename(s). The following specifiers are supported:

              • %a, antenna (coil) name

              • %b, basename (filename of 1st DICOM file)

              • %c, comments

              • %d, description

              • %e, echo number

              • %f, folder name

              • %i, patient ID

              • %j, seriesInstanceUID

              • %k, studyInstanceUID

              • %m, manufacturer

              • %n, patient name

              • %p, protocol

              • %r, instance number (of 1st DICOM file)

              • %s, series number

              • %t, time

              • %u, acquisition number

              • %v, vendor

              • %x, study ID

              • %z, sequence name

              The default format string is "%p_%e_%4s".

       -i <y/n>
              Ignore derived, localizer and 2D images.

       -l <y/n>
              Losslessly scale 16-bit integers to use maximal dynamic range.

       -m <y/n>
              Merge  slices  from  the  same  series  regardless  of  study  time,  echo,   coil,
              orientation, etc...

       -n <number>
              Only  convert  this  series number. Provide a negative number for listing of series
              numbers in input folder.

       -o <path>
              Output directory where the converted files should be  saved.  If  unspecified,  the
              files are saved within the specified source directory.

       -p <y/n>
              Use Philips precise float (rather than display) scaling.

       -r <y/n>
              Rename instead of convert DICOMs. Useful for organizing images.

       -s <y/n>
              Convert a single file only.

       -t <y/n>
              Save patient details as text notes.

       -u     Update check: attempts to see if newer version is available.

       -v <h/y/n>
              Enable verbose output. "n" for succinct, "y" for verbose, "h" for high verbosity

       -x <y/n>
              Crop images. This will attempt to remove excess neck from 3D acquisitions.

       -z <y/i/n>
              Desired  compression  method.  The  "y"es  option uses the external program pigz if
              available.  The  "i"  option  compresses  the  image  using  the  slower   built-in
              compression routines.

LICENSING

       Copying  and distribution of this file, with or without modification, are permitted in any
       medium without royalty provided the copyright notice and this notice are  preserved.  This
       file  is  offered  as-is, without any warranty.  The dcm2niix project is distributed under
       the BSD 2-Clause License.

AUTHOR

       This manual was developed by Ghislain Antony Vaillant and is maintained by the community

COPYRIGHT

       2020 The dcm2niix contributors