dlevitas / Dcm2Bids

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

dcm2bids

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

Dependencies

• dcm2niix to convert DICOM to NIfTI. You need to install it
  • install instructions
  • Recent release

Install

pip install dcm2bids

Upgrading

pip install --upgrade dcm2bids

TL;DR

1. mkdir <YOUR_FUTURE_BIDS_FOLDER>
2. cd <YOUR_FUTURE_BIDS_FOLDER>
3. dcm2bids_scaffold
4. dcm2bids_helper -d <FOLDER_WITH_DICOMS_OF_A_TYPICAL_SESSION>
5. Build your configuration file with the help of the content of tmp_dcm2bids/helper
6. dcm2bids -d DICOM_DIR -p PARTICIPANT_ID -c CONFIG_FILE for each participants of your study

Follow the tutorial

dcm2bids creates log files inside <YOUR_FUTURE_BIDS_FOLDER>/tmp_dcm2bids/log

bids-validator

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.

Similar projects

Other tools to create BIDS datasets :

• heudiconv
• bidskit
• dac2bids