dcm2niix man page

dcm2niix — DICOM to NifTI converter


dcm2niix [options] <sourcedir>


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.


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

-b <y/n>

Save additional BIDS metadata to a side-car .json file.

-ba <y/n>       anonymize BIDS

-f <format>

Format string for the output filename(s). The following specifiers are supported:

  • %a, antenna (coil) number
  • %c, comments
  • %d, description
  • %e, echo number
  • %f, folder name
  • %i, patient ID
  • %j, seriesInstanceUID
  • %k, studyInstanceUID
  • %m, manufacturer
  • %n, patient name
  • %p, protocol
  • %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.

-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.

-s <y/n>

Convert a single file only.

-t <y/n>

Save patient details.

-v <h/y/n>

Enable verbose output. "n" for succinct, "y" for verbose, "h" for high verbosity

-x <y/n>

Crop images.

-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.


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.


This manual was developed and is maintained by Ghislain Antony Vaillant <ghisvail@gmail.com>

Referenced By


Jul 24, 2019 1.0