Welcome to SML fMRI Preprocessing Template Documentation

This documentation covers the Stanford Memory Lab’s fMRI preprocessing template, a generalizable workflow for consistency within and across lab projects.

Overview

The SML fMRI Preprocessing Template transforms internal fMRI preprocessing scripts into a generalizable workflow that handles:

• Automated transfer of scanner acquisitions from FlyWheel to Server

• Raw to BIDS format conversion

• DICOM to NIfTI conversion with dcm2niix

• Dummy scan removal

• Fieldmap-based susceptibility distortion correction setup

• fMRIPrep anatomical and functional workflows

• Interactive TUI launcher for pipeline steps

Quick Start

1. Click “Use this template” to create your own repository

2. Clone your new repository

3. Copy settings.template.sh to settings.sh and customize

4. Follow the configuration guide below

Contents:

• Installation
  • Prerequisites
  • Getting Started
  • System Requirements
  • Next Steps
• Configuration
  • Configuration File
  • Path Configuration
  • Task Parameters
  • Data Validation
  • Fieldmap Mapping
  • Subject Lists
  • Slurm Configuration
  • fMRIPrep Settings
  • Permissions
  • Validation
  • Common Issues
  • Next Steps
• Usage
  • Interactive TUI Launcher
  • Manual Execution
  • Pipeline Steps
  • Monitoring Jobs
  • Quality Control
  • Troubleshooting
  • Best Practices
  • Next Steps
• Workflows
  • Pipeline Overview
  • Workflow Details
  • Data Organization
  • Workflow Customization
  • Advanced Topics
  • Best Practices
  • Next Steps
• Contributing
  • Contributing to the SML fMRI Preprocessing Template
  • Commit Message Guidelines
  • Release Process
  • Development Workflow
  • Code Review Process
  • Changelog Maintenance
  • Documentation
  • Questions?
• Changelog
  • Changelog
• Privacy Policy
  • Analytics and Data Collection

Features

✅ Automated Transfer

Transfer scanner acquisitions from FlyWheel to Server

✅ BIDS Conversion

Convert raw data to BIDS format

✅ DICOM to NIfTI

Use dcm2niix for conversion

✅ Dummy Scan Removal

Remove initial dummy scans

✅ Distortion Correction

Fieldmap-based susceptibility distortion correction

✅ fMRIPrep Integration

Run anatomical and functional workflows

✅ Interactive TUI

User-friendly launcher for pipeline steps

✅ Quality Control

Built-in validation and QC utilities

Getting Help

• GitHub Issues

• Contributing Guidelines

• Stanford Memory Lab

Indices and tables

• Index

• Module Index

• Search Page