Add optional smoothing Fix #212

[jpillai00]

Adds --smooth FWHM flag to rbc metrics, rbc functional, rbc all, rbc longitudinal metrics, rbc longitudinal functional, and rbc longitudinal all to control smoothing of derivative outputs and cleaned BOLD.

Changes:

• Smoothing is now optional - raw maps and z-scored raw maps (desc-zstd) are always produced. When --smooth FWHM is set, the following are additionally exported:
  • Derivative maps: smoothed (desc-sm{fwhm}) and z-scored smoothed (desc-sm{fwhm}Zstd)
  • Cleaned BOLD: smoothed (desc-sm{fwhm}preproc), export-only, applied post-regression and bandpass filtering
• FWHM label formatting handles both whole numbers (6.0 -> sm6) and non-integer values (0.1 -> sm0p1) for BIDS compliance
• Moved smooth from rbc.core.metrics.smoothing to rbc.core.common
  • verified via 3dBlurToFWHM that it correctly handles both 3D derivative maps and 4D BOLD timeseries
• Added tests for smoothed BOLD and map exports

[github-actions]

Tests	Skipped	Failures	Errors	Time
786	0 💤	0 ❌	0 🔥	11.525s ⏱️

[Copilot]

Pull request overview

Adds an optional --smooth FWHM parameter across rbc metrics, rbc functional, and rbc all so that smoothing is no longer always performed; raw + z-scored raw derivatives are always produced, and smoothed variants are emitted only when requested.

Changes:

• Replace required/default smoothing (fwhm=6.0) with optional smooth: float | None throughout CLI args, orchestration, and workflows.
• Update metrics workflow outputs to always include raw + z-scored raw maps, and optionally include smoothed + z-scored smoothed maps.
• Extend export + test coverage for conditional smoothed outputs and correct BIDS desc- label construction.

Reviewed changes

Copilot reviewed 16 out of 16 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
tests/unit/orchestration/test_functional.py	Updates orchestration test to use smooth instead of fwhm.
tests/unit/cli/test_metrics.py	Updates metrics CLI tests for --smooth default/validation and parser wiring.
tests/unit/cli/test_functional.py	Adds smooth to functional CLI namespace fixture.
tests/unit/cli/test_all.py	Updates all CLI tests for --smooth default/validation and parser wiring.
tests/unit/bids/test_exports.py	Updates export fixtures/count assertions; adds tests for conditional smoothed exports and desc labels.
tests/full_pipeline/test_metrics.py	Adjusts pipeline test to tolerate optional (None) outputs.
src/rbc/workflows/metrics.py	Makes smoothing optional; always computes z-scored raw maps; adds optional smoothed + z-scored smoothed outputs.
src/rbc/workflows/functional.py	Adds optional smoothing path for cleaned BOLD export.
src/rbc/orchestration/metrics.py	Threads smooth through orchestration and passes it into exports.
src/rbc/orchestration/functional.py	Threads smooth through functional orchestration and exports.
src/rbc/orchestration/all.py	Threads smooth through the combined pipeline for metrics exporting.
src/rbc/cli/metrics.py	Renames --fwhm to --smooth, makes it optional, and updates validation/args.
src/rbc/cli/functional.py	Adds optional --smooth to functional CLI and passes through to orchestration.
src/rbc/cli/all.py	Renames --fwhm to --smooth, makes it optional, and updates validation/args.
src/rbc/bids/metrics.py	Exports raw + z-scored raw always; conditionally exports smoothed variants when smooth is set.
src/rbc/bids/functional.py	Conditionally exports smoothed cleaned BOLD when requested.

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[nx10]

There is a missing period in mm (e.g. --smooth 6.0) copy pasted 6 times.
Otherwise it looks good to merge! - could you rebase so the CI runs over this again?