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

       -ba <y/n> anonymize BIDS (default y).
              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

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

       2022 The dcm2niix contributors