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[ENH] How to handle fMRIPrep's outputs for multi-session data without causing errors of merging/unzipping? #23

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zhao-cy opened this issue Feb 1, 2023 · 0 comments · May be fixed by #75
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zhao-cy commented Feb 1, 2023

Problem/Challenge:

  • In recent version of fMRIPrep, seems it does not incorporating session names in some of the output files (e.g., html files, freesurfer outputs), which results in same filenames from different sessions in multi-session dataset. If not renaming those files, it will further cause merging problem (if did not zip results) or error when unzipping .
  • The output names of fMRIPrep may be also different across different versions, so there may not be a universal solution for all versions of fMRIPrep

Potential solution:
Initial idea was recorded in issue #3. In detail, to rename files after datalad run of the container, based on configurations specified in container config YAML fle, merge-conflict-files or so, TBD. In this section:

  • either defines the file patterns that should be renamed (or removed), and BABS will rename them based on BIDS(ish) standard;
  • or, lists the specific mv command to use for renaming;

We plan to provide example YAML file which is compatible with fMRIPrep's most recent stable version; we probably need effort from others (other developers and users) to add YAML file for older versions.

@zhao-cy zhao-cy linked a pull request Apr 12, 2023 that will close this issue
@zhao-cy zhao-cy linked a pull request Apr 13, 2023 that will close this issue
@zhao-cy zhao-cy linked a pull request Apr 17, 2023 that will close this issue
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