Dcm2Bids helps you to convert DICOM files of a study to Brain Imaging Data Structure (BIDS).
Learn more about BIDS and read the specifications.
git clone https://github.com/cbedetti/Dcm2Bids
Add the installation directory to your PYTHONPATH and the scripts
directory to your PATH.
- dcm2niix
DICOM to NIfTI conversion is done with dcm2niix
converter. See their github for source or NITRC for compiled versions.
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.
The description field is a list of dictionnary. Each dictionnary describes one acquisition.
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.