dcm2bids reorganises NIfTI files from dcm2niix into the Brain Imaging Data Structure (BIDS).
Before using this software, learn more about BIDS:
- read the BIDS specifications and the paper
- some dataset examples
- dcm2niix to convert DICOM to NIfTI. You need to install it
pip install dcm2bids
pip install --upgrade dcm2bids
mkdir <YOUR_FUTURE_BIDS_FOLDER>cd <YOUR_FUTURE_BIDS_FOLDER>dcm2bids_scaffolddcm2bids_helper -d <FOLDER_WITH_DICOMS_OF_A_TYPICAL_SESSION>- Build your configuration file with the help of the content of
tmp_dcm2bids/helper dcm2bids -d DICOM_DIR -p PARTICIPANT_ID -c CONFIG_FILEfor each participants of your study
Follow the tutorial
dcm2bids creates log files inside <YOUR_FUTURE_BIDS_FOLDER>/tmp_dcm2bids/log
Run the bids-validator to check your directory. Don't forget to create a .bidsignore file at the root of your BIDS directory with tmp_dcm2bids/* inside.
Other tools to create BIDS datasets :