v0.3.0 - Docker Support & 14-Step Pipeline

fMRIPrep Workbench v0.3.0

🚀 Major Features

🐳 Docker Containerization

• Complete Docker support with multi-platform images (linux/amd64, linux/arm64)
• Easy-to-use wrapper script with commands: start, stop, launch, shell, logs, status
• Docker Compose configuration for streamlined deployment
• Singularity/Apptainer support for HPC clusters
• Automated CI/CD pipeline to Docker Hub

📊 FSL FEAT Statistical Analysis (Steps 10-13)

• Complete GLM analysis workflow (Level 1, 2, 3)
• Interactive setup utility with model configuration
• Support for condition keys, contrasts, and confound regressors
• SLURM array job integration for parallel processing

🧠 FreeSurfer Manual Editing Workflow (Steps 7-8)

• Download/upload utilities for manual surface editing
• Automatic timestamped backups before upload
• Support for batch operations on multiple subjects
• Interactive and non-interactive modes

📚 Documentation Migration

• Migrated from Sphinx (RST) to MkDocs (Markdown)
• Material theme with dark mode support
• PDF export capability
• Improved navigation and search

🔢 14-Step Pipeline Architecture

Complete end-to-end workflow from acquisition to analysis:

• Steps 1-6: Download, conversion, prep, QC
• Steps 7-8: FreeSurfer editing workflow
• Step 9: Full fMRIPrep execution
• Steps 10-13: FSL FEAT GLM analysis
• Step 14: Data management utilities

🐛 Bug Fixes

• Subject list processing: Filter comments and empty lines
• DICOM conversion: Multi-session handling, single-echo sequences
• QC scripts: Write logs to correct directory
• File handle leaks: Use context managers in FSL GLM scripts
• Container management: Replace fixed delays with readiness polling

💥 Breaking Changes

• Directory renaming: 07-run-fmriprep → 09-run-fmriprep, 08-fsl-glm → 10-fsl-glm
• Pipeline structure: Expanded from 7 to 14 steps
• Documentation format: Changed from Sphinx to MkDocs

📦 Installation

Docker (Recommended)

docker pull shawnschwartz/fmriprep-workbench:0.3.0

Singularity (HPC Clusters)

Download the .sif file from the release assets below.

See the documentation for complete installation and usage instructions.

📖 Documentation

• Installation Guide
• Docker Usage Guide
• Configuration Guide
• Full Documentation

Full Changelog: v0.1.8...v0.3.0

Release v0.1.1

What's Changed

🚀 Features

🐛 Bug Fixes

Fix: Add parameter configs for diagnostic toolbox options 9 and 10

📚 Documentation

🔧 Maintenance

💥 Breaking Changes

• No breaking changes

Full Changelog: v0.1.0...v0.1.1

Release v0.1.0

What's Changed

🚀 Features

• feat(01-prepare): add core prepare_fmri.sh script
• feat(01-prepare): add core update_fmap_metadata.py script
• feat(01-prepare): add core submit_job.sbatch executable
• feat(fmriprep): test scripts
• feat: gracefully skip missing bold runs instead of quitting
• feat: add dynamic subject txt files to pipeline steps
• feat: add new pull_fmriprep_reports utility script in the new tools/ directory
• feat(TUI): add interactive launcher component
• feat: frontend work on flywheel downloader utility script
• feat: add changelog, release workflow automation, and ReadTheDocs integration

🐛 Bug Fixes

📚 Documentation

• docs: add README for documentation directory

🔧 Maintenance

• chore: update gitignore
• chore: update LICENSE
• chore: add contributing guidelines
• chore(readme): add first complete draft with info and instructions
• chore(README): fix markdown table formatting issues
• chore: relocate job submitter script
• chore: update settings template
• chore: clean up slurm args in submit_01.sbatch
• chore: rename sbatch run file
• chore: clean up INFO logs in 01-run.sbatch
• chore: clean up log messages in prepare_fmri.sh
• chore: make update_fmap_metadata.py executable
• chore: update logging methods
• chore: restructure subjects.txt files
• chore: update values in settings.template.sh
• chore: restructure subjects template file
• chore: update subjects txt file approach
• chore: add new log statements
• chore: update readme
• chore: update 01-run.sbatch
• chore: update 02-run.sbatch
• chore: update README.md
• chore: lint prepare_fmri.sh
• chore: fix #5
• chore: lint fmriprep.sh
• refactor: migrate fw-downloader to independent step
• refactor(sbatch): run scripts
• refactor(launch): window with new options

💥 Breaking Changes

• No breaking changes

Full Changelog: v0.0.0...v0.1.0