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
Options: isGz: false isFlipY: false isVerbose: false isCreateBIDS: false isOnlySingleFile: false Files: - 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
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 <firstname.lastname@example.org>
2021 The dcm2niix contributors