SML fMRI Preprocessing Template
Contents:
Installation
Prerequisites
Getting Started
System Requirements
Next Steps
Configuration
Configuration File
Path Configuration
Task Parameters
Data Validation
Fieldmap Mapping
Subject Lists
Subject ID Modifiers
Slurm Configuration
fMRIPrep Settings
Permissions
Validation
Common Issues
Next Steps
Usage
Interactive TUI Launcher
Manual Execution
Basic Usage
fMRIPrep Options
Pipeline Steps
Monitoring Jobs
Check Slurm Job Status
Check Logs
Quality Control
Troubleshooting
Failed Jobs
Rerunning Subjects
Debug Mode
Best Practices
Next Steps
Workflows
Pipeline Overview
Workflow Details
1. FlyWheel Transfer (01-fw2server)
2. BIDS Conversion (02-bidsify)
3. DICOM to NIfTI (03-dcm2niix)
4. Prep for fMRIPrep (04-prep-fmriprep)
5. fMRIPrep Anatomical (05-run-fmriprep)
6. fMRIPrep Complete (06-run-fmriprep)
Data Organization
Output Structure
Workflow Customization
Per-Subject Control
Resource Configuration
Advanced Topics
Parallel Processing
Output Spaces
Manual Interventions
Best Practices
Next Steps
Contributing
Contributing to the SML fMRI Preprocessing Template
Welcome!
How Can I Contribute?
Scientific Contributions
Technical Contributions
Contribution Process
Pull Request Guidelines
Commit Message Guidelines
Format
Types
Breaking Changes
Examples
Release Process
Questions?
Commit Message Guidelines
Commit Message Format
Types
Breaking Changes
Examples
Scope
Release Process
Manual Release
Version Numbering
Development Workflow
1. Fork and Branch
2. Make Changes
3. Test Locally
4. Commit Changes
5. Push and Create PR
Code Review Process
Changelog Maintenance
Documentation
Questions?
Changelog
Changelog
Unreleased
0.2.0 - 2025-12-18
🚀 Features
🐛 Bug Fixes
📚 Documentation
🔧 Maintenance
💥 Breaking Changes
0.1.7 - 2025-12-18
🚀 Features
🐛 Bug Fixes
📚 Documentation
🔧 Maintenance
💥 Breaking Changes
0.1.6 - 2025-12-18
🚀 Features
🐛 Bug Fixes
📚 Documentation
🔧 Maintenance
💥 Breaking Changes
0.1.5 - 2025-12-18
🚀 Features
🐛 Bug Fixes
📚 Documentation
🔧 Maintenance
💥 Breaking Changes
0.1.4 - 2025-12-18
🚀 Features
🐛 Bug Fixes
📚 Documentation
🔧 Maintenance
💥 Breaking Changes
0.1.3 - 2025-12-18
🚀 Features
🐛 Bug Fixes
📚 Documentation
🔧 Maintenance
💥 Breaking Changes
0.1.2 - 2025-12-17
🚀 Features
🐛 Bug Fixes
📚 Documentation
🔧 Maintenance
💥 Breaking Changes
0.1.1 - 2025-12-17
🚀 Features
🐛 Bug Fixes
📚 Documentation
🔧 Maintenance
💥 Breaking Changes
0.1.0 - 2025-12-17
🚀 Features
🐛 Bug Fixes
📚 Documentation
🔧 Maintenance
💥 Breaking Changes
Added
1.0.0 - 2024-12-17
Added
Features
Privacy Policy
Analytics and Data Collection
What We Collect
Purpose of Data Collection
What We Do NOT Collect
Data Privacy and Retention
Opting Out
For Researchers and Institutional Users
Questions or Concerns
SML fMRI Preprocessing Template
Index
Index