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README.md

dcm2bids

PyPI version Documentation DOI

Code style: black

dcm2bids reorganises NIfTI files from dcm2niix into the Brain Imaging Data Structure (BIDS).

Before using this software, learn more about BIDS:

Dependencies

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 :

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