Welcome to BIC 3T MRI Pipeline HPC’s documentation!

Contents:

• About
  • The BIDS format and BIDS-App pipelines
• Usage
  • Running on one node
  • Running FreeSurfer-informed FSL DTI tractography on GPU
  • Metrics Collation
  • (Optional) HTML Quality Control Report Generator
  • Preparing your dataset for sharing
• Main Pipeline
  • Inputs
  • Outputs
    • Preprocessing derivatives
    • Analyses derivatives
    • Metrics:
    • Preparing your dataset for sharing
    • FSL DTI probabilistic tractography from QSIPrep Preprocessing (Optional)
    • (Optional) HTML Quality Control Report Generator
• Sub-Pipelines
  • BIDS-App containers
    • MRIQC - Anatomical & Functional Quality Control
    • fMRIPrep - Anatomical & Functional Preprocessing
    • XCPEngine - Correlation-based resting-state functional connectivity analysis
    • QSIPrep - DWI preprocessing and reconstruction
    • FSL DTI probabilistic tractography from QSIPrep Preprocessing
• Heuristics
• Install
• FAQs
  • How to build with Docker
  • How to build with Singularity
• Troubleshooting
• Troubleshooting
  • Container building
    • Singularity cache and tmp
    • SquashFS-tools
  • Container running
    • TemplateFlow
• Manual-Correction
• Citing
  • The Original Beckman Processing Pipeline Working Group:
• Requests

Indices and tables

• About

• Usage

• Install

• FAQs

• Troubleshooting

• Manual-Correction

• Citing

• Requests

• Search Page