pl-dcm2niix ChRIS Plugin

pl-dcm2niix is a ChRIS ds plugin wrapper around dcm2niix. It converts an input directory of DICOMs into an output directory of NIFTI images. Also, dcmdjpeg is bundled for convenient handling of JPEG-compressed DICOM files.

Usage

pl-dcm2niix can run from ChRIS or locally on the command-line using Apptainer.

apptainer exec docker://fnndsc/pl-dcm2niix dcm2niixw input/ output/

A subset of the options from the original dcm2niix are available.

Examples

Example datasets can be obtained from here:

https://github.com/DataCurationNetwork/data-primers/blob/main/Neuroimaging%20DICOM%20and%20NIfTI%20Data%20Curation%20Primer/neuroimaging-dicom-and-nifti-data-curation-primer.md#example-datasets

To convert DICOMs in inputdir/ to NIFTIs in outputdir/, without producing BIDs sidecar JSON (-b n), disable automatic 2D slice merge (-m n), compressed .nii.gz output (-z y):

apptainer exec docker://fnndsc/pl-dcm2niix dcm2niixw -b n -m n -z y inputdir/ outputdir/

Pre-process all *.dcm files using dcmdjpeg before running dcm2niix:

apptainer exec docker://fnndsc/pl-dcm2niix dcm2niixw --dcmdjpeg inputdir/ outputdir/

Tip

The command dcmdjpeg is a no-op on already decoded files, i.e. it's okay to use dcmdjpeg when inputdir/ contains a mix of JPEG-compressed and ordinary DICOM files.