dcm2niibatch - Man Page

DICOM to NifTI batch converter


dcm2niixbatch <configuration-file>


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.

dcm2niibatch acts as a wrapper around dcm2niix and allows the processing of multiple DICOM sequences by specifying the list of files and settings in a yaml text file. The makes processing a dataset of DICOM scans simpler and more easily repeatable.

In addition, yaml files are designed to be both human and machine readable and a script can easily be written in many programming languages to automatically create a yaml file based on an existing folder structure.

Please be advised that dcm2niix and dcm2niibatch have been developed for research purposes only and should not be considered a clinical tool.

Configuration File Format

Perform a batch conversion of multiple dicoms using dcm2niibatch, which is run by passing a configuration file e.g dcm2niibatch batch_config.yml

The configuration file should be in yaml format as shown in example batch_config.yaml

  isGz:             false
  isFlipY:          false
  isVerbose:        false
  isCreateBIDS:     false
  isOnlySingleFile: false
      in_dir:           /path/to/first/folder
      out_dir:          /path/to/output/folder
      filename:         dcemri
      in_dir:           /path/to/second/folder
      out_dir:          /path/to/output/folder
      filename:         fa3

You can add as many files as you want to convert as long as this structure stays consistent. Note that a dash must separate each file.

in_dir     Path to the dicom files

out_dir    Path to save the nifti file

filename   File name of nifti file to save

See Also



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 Benjamin Irving <mail@birving.com>


Jan 26, 2021 1.0 dcm2niix