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