con / con/mechababs

fs-license is bound twice in the generated invocation; the YAML comment is stale

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automation pipeline:fmriprep
Dominant language
Python
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1
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15h 39m
Merged PRs (30d)
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Description

The rendered `bids-fmriprep_zip.sh` binds the FreeSurfer license **twice**: once emitted by babs itself, and once from our pipeline `singularity_args`. Observed in the 2026-07-19 Unity run:

```
-B /license.txt:/SGLR/FREESURFER_HOME/license.txt
```

Same source, same destination, so **nothing breaks** — the duplicate bind only produces a warning. But it means **current babs main does auto-bind the fs-license**, and the comment in the fmriprep/mriqc pipeline YAMLs — "BABS rewrites `--fs-license-file` ... does NOT auto-bind, so we bind manually" — is stale.

## Cleanup

Drop the manual `-B .../license.txt:/SGLR/FREESURFER_HOME/license.txt` from the fmriprep + mriqc `singularity_args`, and correct the comment.

## Why it is not a quick commit

Verification needs a **real fmriprep or mriqc run** to confirm babs's own bind is sufficient. The e2e uses simbids, which does not consume a FreeSurfer license, so the local suite cannot exercise it natively (a hacked-up simbids config could approximate it). So this waits for a run that already needs doing, rather than motivating one.

Also a concrete data point for the pipeline-vs-cluster config composition question, which already carries the fs-license rewrite as a case.

Contributor guide

No contributing guide indexed for this repository

Research direction

Inspect the fmriprep and mriqc pipeline YAMLs, focusing on singularity_args and the stale fs-license comment; compare their output with the generated bids-fmriprep_zip.sh invocation. Remove the duplicate bind and confirm with a real fmriprep or mriqc run that babs's auto-bind is sufficient.

Written by the indexing model from the issue text.

Assessment

Tech stack
shell, yaml
Domain
devops, infrastructure
Issue type
Refactor
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
45/100

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