con / con/mechababs

Drop or hold the `resampling` fmriprep stage?

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blocked decision pipeline:fmriprep
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Python
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Description

# Drop or hold the `resampling` fmriprep stage?

> **Blocked by:** fmriprep confounds-at-resampling release (Chris Markiewicz, external)

## Decision

`fmriprep --level resampling` is currently **redundant with minimal**
(resampling ≡ minimal in fmriprep 25.2.5 — Chris Markiewicz, 2026-05-19).
Decide: **drop** the stage, or **hold it as a no-op** until Chris ships the
confounds-at-resampling change (the cheap confounds — motion, FD/DVARS, WM/CSF
ROI means — move into resampling), at which point it gains value.

Leaning: **hold as a no-op** for now.

## Evidence (folds in the two stale "Resample question" notes)

- resampling ≡ minimal in current fmriprep; cheap confounds planned for a future
release; CompCor stays at `full` (Chris, 2026-05-19). The "Resample question"
in our fmriprep meeting notes is stale against this — update/retire it.
- `--cifti-output 91k` was added to the resampling YAML post-run; no rerun to
verify. But the asymmetric diff (minimal had cifti, resampling didn't) showed
**zero functional difference** — empirical evidence that resampling ignores
cifti gating in 25.2.5, independently supporting Chris's claim.

## Blocked

On Chris shipping confounds-at-resampling (external fmriprep release) — revisit
the drop/hold call then.

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by reviewing the issue's evidence about fmriprep 25.2.5, including the minimal/resampling comparison and the stale “Resample question” meeting notes. The work is blocked on Chris Markiewicz's external confounds-at-resampling release; done means revisiting the drop-versus-no-op decision after that release.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Refactor
Difficulty
5/5
Estimated time
Over a week
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
25/100

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