add stages to long_fastsurfer.sh

[m-reuter]

Enhancement requested #780

Summary

Adds stage-based execution to long_fastsurfer.sh, allowing users to run individual pipeline stages independently for flexible resource allocation across compute nodes with varying GPU/CPU capabilities.

Changes

• Added --stage flag to select which stages to run: prepare, template_seg, template_surf, long_seg, long_surf, or all (default)
• Automatic dependency validation ensures required stages have completed before running dependent stages
• Smart input validation: only requires --t1s when running prepare stage
• Backward compatible: default behavior unchanged (runs all stages)

Usage

# Run full pipeline (default, unchanged)
./long_fastsurfer.sh --tid template01 --t1s tp1.mgz tp2.mgz --tpids tp1 tp2

# Run individual stage
./long_fastsurfer.sh --tid template01 --tpids tp1 tp2 --stage template_seg

# Run multiple stages
./long_fastsurfer.sh --tid template01 --tpids tp1 tp2 --stage template_surf --stage long_surf

Benefits

• Resource optimization: Send GPU stages to GPU nodes, CPU stages to CPU nodes
• Restart capability: Re-run individual stages without reprocessing completed ones
• Better cluster scheduling: Split heavy jobs into smaller, faster-to-schedule jobs

[Copilot]

Pull request overview

This PR enhances the longitudinal pipeline driver long_fastsurfer.sh by adding a --stage flag to run individual pipeline stages independently (or the full pipeline by default), enabling splitting work across different compute resources (CPU/GPU) and improving restartability.

Changes:

• Added stage selection (--stage) with a set of named pipeline stages and updated help text.
• Added stage dependency checks and stage-aware input validation (e.g., only requiring --t1s for prepare).
• Wrapped each pipeline block (prepare, template_seg, template_surf, long_seg, long_surf) behind stage gating logic.

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[Copilot]

Pull request overview

Copilot reviewed 1 out of 1 changed files in this pull request and generated 1 comment.

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[dkuegler]

I think I would use should_run_stage also in the validation check function.
And at the end only print "Full" if it is actually the final stage.

[dkuegler]

Looks good to me 👍