dcm2niix - DICOM to NifTI converter

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

       2024 The dcm2niix contributors

1.0                                               Nov 19, 2024                                       DCM2NIIX(1)

       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.

       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.

       dcm2niix - DICOM to NifTI converter

       -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 (default y).  The "i"nput-only option reads
              DICOMs but saves neither BIDS nor NIfTI.

       -ba<y/n>anonymizeBIDS(defaulty).
              If "n"o, side-car may report patient name, age and weight.

       -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, series instance UID

              • %k, study instance UID

              • %m, manufacturer

              • %n, patient name

              • %o, media object instance UID

              • %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".

       -g<y/n/o/i>
              Generate defaults file (default n) If "y", create default file on completion If "n", default  will
              not  be  written If "o", only reset and write defaults If "i", the values of the defaults file are
              ignored : reset defaults], default n)

       -h     Show help

       -i<y/n>
              Ignore derived, localizer and 2D images (default n)

       -l<y/n/o>
              Losslessly scale 16-bit integers to use maximal dynamic range (default o).  If "y", then intensity
              rescaled to use full 16-bit range.  If "n", data not scaled uint16 will be  saved  as  int16.   If
              "o", original data and datatype preserved.

       -m<y/n/2>
              Merge slices from the same series regardless of study time, echo, coil, orientation, etc. (default
              2).  If "2", automatic based on image modality.

       -n<number>
              Only  convert  this series CRC number. Provide a negative number for listing of series CRC 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<2/y/n>
              Enable verbose output. "n" for succinct, "y" for verbose, "2" for high verbosity

       -x<y/n/i>
              Crop  images.  This  will  attempt to remove excess neck from 3D acquisitions.  If "i", images are
              neither cropped nor rotated to canonical space.

       -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.

       --big-endian<y/n/o>
              Byte order (default o). Optimal is machine native

       --progress
              Slicer format progress information (y/n, default n)

       --ignore_trigger_times
              Disregard values in 0018,1060 and 0020,9153

       --terse
              Omit filename post-fixes (can cause overwrites)

       --version
              Report version and terminate

       --xml  Slicer format features

dcm2niix [options] <sourcedir>