Is there any way to use dcm2bids or neudiconv with Python?


I try to use dcm2bids or heudiconv to use fMRIprep at the end.

  1. Anyway, will you recommend any program converting dicom to bids?
    The data I have has different sessions from person to person, so it is hard to handle.

  2. In addition, is it possible to use dcm2bids or heudiconv with Python (Jupyter notebook)?
    Most of tutorials are done with MacOS, and handling multiple session in Linux is quite hard for me.

  3. If it is possible, can you attach a code example of handling multiple sessions?

  4. Is there any tips to organize folders before using dcm2bids or heudiconv when handling multiple subjects, multiple sessions?


Hi @_JY

Thank you for your question! Please find answers to your questions below:

  1. Using dcm2bids or HeuDiConv are good converting programs. Depending on the size of your set, this could be a combination of using automated programs and a custom solution. We have tutorials for converting data into BIDS: showing a more custom solution and using HeuDiConv

  2. HeuDiConv uses a file so not explicitly with python with but using it. The easiest way is using a docker image. Dcm2bids appears to be command-line mostly. I have not seen a jupyter notebook implementation but we have a BIDS starter kit that can be useful to look through!

  3. The HeuDiConv tutorial showed a single subject with multiple sessions

  4. Regarding folder organization pre-dcm2bids or HeuDiConv would be what makes making the programmatic solution more easier to implement and script

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