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PennLINC / xcp_d

Post-processing of fMRIPrep, NiBabies, and HCP outputs
https://xcp-d.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Add `--longitudinal` flag to process anatomical data separately for each session #1098

Closed tsalo closed 2 months ago

tsalo commented 6 months ago

Summary

By default, fMRIPrep averages anatomical images across sessions. However, there may be some situations in which the preprocessing pipeline produces session-wise anatomical data (e.g., #1090, longitudinal studies like HBCD).

Additional details

The longitudinal pipeline requires session-level anatomical derivatives. It's possible that we could automatically configure the pipeline based on the organization of the data.

Next steps

  1. If the --longitudinal flag is used, do the following:
    1. Search the dataset for anatomical images on a session-wise basis, and process them independently.
    2. Output figures in sub-X/ses-X/figures folder.
    3. Output session-wise HTML reports. Where should this go? In xcp_d/ or xcp_d/sub-X/ or xcp_d/sub-X/ses-X?
    4. If there is a subject-level anatomical folder, then only allow a single session (from Damien).
  2. If the flag is not used, do the following:
    1. Look for a single set of preprocessed anatomical images at the subject level (not the session level).
    2. Output figures in sub-X/figures folder.
    3. Output a single subject-level HTML report.
tsalo commented 6 months ago

Related Nibabies issue: https://github.com/nipreps/nibabies/issues/350

tsalo commented 2 months ago

Actually I don't think this is necessary since we have --aggregate-session-reports.