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Add --session-id parameter and support longitudinal output structure #3265

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Add --session-id parameter and support longitudinal output structure #3265

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tsalo
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@tsalo tsalo commented Mar 29, 2024 •
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Closes nipreps/smriprep#429. I've only just started on this, and it won't deal with lingering longitudinal issues, such as:

  1. Writing out session-level HTML reports to the subject's session folder.
    • Not sure how I feel about this one TBH.
  2. Writing out session-level figures to the subject's session folder (see HTML report folder structure does not work for ongoing longitudinal out of the box nibabies#350).
  3. Running FreeSurfer on a session-wise basis (see Alter FreeSurfer subjects to include session labels nibabies#288).

Changes proposed in this pull request

  • Add --session-id command line parameter.
  • Copy over longitudinal organization code from Nibabies.
    • In order to collect session-wise anatomical derivatives, we need to either add a session_id parameter to smriprep.utils.bids.collect_derivatives() or adopt Nibabies' nibabies.utils.bids.Derivatives class. Which is better?

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codecov bot commented Mar 29, 2024

Codecov Report

Attention: Patch coverage is 61.11111% with 14 lines in your changes are missing coverage. Please review.

Project coverage is 66.50%. Comparing base (8eb8215) to head (1672988).

Files Patch % Lines
fmriprep/workflows/base.py 18.18% 9 Missing ⚠️
fmriprep/cli/parser.py 88.23% 2 Missing ⚠️
fmriprep/cli/workflow.py 0.00% 2 Missing ⚠️
fmriprep/config.py 83.33% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##           master    nipreps/fmriprep#3265      +/-   ##
==========================================
- Coverage   73.62%   66.50%   -7.13%     
==========================================
  Files          56       56              
  Lines        4243     4266      +23     
==========================================
- Hits         3124     2837     -287     
- Misses       1119     1429     +310

☔ View full report in Codecov by Sentry.
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@tsalo tsalo closed this Jun 21, 2024
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Enable longitudinal structural analysis
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@tsalo