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
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© Copyright 2025, Shawn Schwartz and Stanford Memory Lab.

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