diegoangls/dcm2bids

Convert DICOM images to BIDS

Dcm2Bids

Dcm2Bids helps you to convert DICOM files of a study to Brain Imaging Data Structure (BIDS).

Learn more about BIDS and read the specifications.

Install

git clone https://github.com/cbedetti/Dcm2Bids

Add the installation directory to your PYTHONPATH and the scripts directory to your PATH.

Software dependencies

• dcm2niix

DICOM to NIfTI conversion is done with dcm2niix converter. See their github for source or NITRC for compiled versions.

Usage

dcm2bids [-h] -d DICOM_DIR -p PARTICIPANT [-s SESSION] -c CONFIG
         [--dry_dcm2niix] [-y]

You need to build the config file of your study to let dcm2bids associate your acquisitions with the right dicoms through bids sidecar created by dcm2niix. Every study is different and this step needs a little bit of work.

The configuration uses the json format and one example is provided in the example directory.

Descriptions

The description field is a list of dictionnary. Each dictionnary describes one acquisition.

Output

dcm2bids create sub-<PARTICIPANT> directories in the folder the script is launched.

Acquisitions with no or more than one fitting descriptions are kept in tmp_dcm2niix directory. Users can review these missing acquistions to change the configuration file accordingly.