dcm2niibatch - DICOM to NifTI batch converter
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.
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
developed for research purposes only and should not be considered a clinical
Perform a batch conversion of multiple dicoms using dcm2niibatch
is run by passing a configuration file e.g dcm2niibatch
The configuration file should be in yaml format as shown in example
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
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
2017 The dcm2niix contributors