Expand pipeline to 14 steps and update documentation#55
Conversation
The pipeline has been restructured and expanded from 7 to 14 steps, now including dedicated FreeSurfer manual editing utilities, FSL FEAT statistical analysis (Level 1-3), and a tarball utility for data management. All documentation (README, configuration, installation, usage, workflows, and toolbox guides) has been updated to reflect the new step numbering, expanded workflow, and migration from settings.sh to config.yaml. Instructions, tables, and examples now cover the full preprocessing and analysis workflow, including manual FreeSurfer editing and statistical analysis.
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Pull request overview
This PR expands the fMRIPrep preprocessing pipeline from 7 to 14 steps and migrates configuration from settings.sh to config.yaml. The expansion includes dedicated FreeSurfer manual editing utilities (steps 7-8), FSL FEAT statistical analysis (steps 10-13), and a tarball utility for data management (step 14). All documentation has been updated to reflect the new step numbering, expanded workflow capabilities, and YAML-based configuration system.
Key changes:
- Pipeline expanded from 7 to 14 steps with new FreeSurfer editing, FSL FEAT analysis, and data management capabilities
- Configuration migrated from Bash (
settings.sh) to YAML (config.yaml) with corresponding updates throughout documentation - Documentation comprehensively updated across README, installation guide, usage guide, workflows guide, configuration guide, and developer documentation (CLAUDE.md)
Reviewed changes
Copilot reviewed 8 out of 8 changed files in this pull request and generated 17 comments.
Show a summary per file
| File | Description |
|---|---|
| toolbox/README.md | Updated configuration references from settings.sh to config.yaml with load_config.sh loader |
| docs/workflows.md | Expanded pipeline overview from 7 to 14 steps with detailed table including FreeSurfer editing and FSL FEAT analysis steps |
| docs/usage.md | Updated all step numbering and added comprehensive workflow examples for standard processing, FreeSurfer editing, and FSL FEAT analysis |
| docs/installation.md | Updated migration guide to reflect 14-step pipeline structure and new step numbering |
| docs/index.md | Updated quick start guide and feature list to cover all 14 pipeline steps |
| docs/configuration.md | Updated fMRIPrep SLURM settings documentation and migration guide with new step references |
| README.md | Contains unresolved merge conflicts - expanded feature list to 14 steps, updated quick start examples, and added FreeSurfer editing utility documentation |
| CLAUDE.md | Comprehensive update to developer documentation covering all 14 steps, configuration system migration, and detailed workflow examples |
Critical Issue: README.md contains unresolved git merge conflict markers that must be resolved before merging.
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| -f surf/rh.white:edgecolor=blue \ | ||
| -f surf/rh.pial:edgecolor=red | ||
| # Make edits to brainmask, white matter, or surfaces | ||
| # Rerun Freesurfer if needed after brainmask/WM edits: |
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Incorrect capitalization. "Freesurfer" should be "FreeSurfer" (with capital F and capital S). This is the official product name capitalization and should be consistent throughout the documentation.
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@copilot open a new pull request to apply changes based on the comments in this thread |
… PR review Co-authored-by: shawntz <5200266+shawntz@users.noreply.github.com>
Co-authored-by: shawntz <5200266+shawntz@users.noreply.github.com>
Fix FreeSurfer capitalization, job naming, and documentation clarity
…riprep, 08-fsl-glm → 10-fsl-glm Co-authored-by: shawntz <5200266+shawntz@users.noreply.github.com>
Fix directory naming to match 14-step pipeline structure
The pipeline has been restructured and expanded from 7 to 14 steps, now including dedicated FreeSurfer manual editing utilities, FSL FEAT statistical analysis (Level 1-3), and a tarball utility for data management. All documentation (README, configuration, installation, usage, workflows, and toolbox guides) has been updated to reflect the new step numbering, expanded workflow, and migration from settings.sh to config.yaml. Instructions, tables, and examples now cover the full preprocessing and analysis workflow, including manual FreeSurfer editing and statistical analysis.