User Guide

• Introduction
  • Requirements to input images
  • System Requirements
  • Expert usage
  • FreeSurfer Downstream Modules
  • Want to know more?
  • Intended Use
  • References
  • Acknowledgements
• Quick Start
  • Segment an example image
  • Google Colab
• Installation
  • Which method should I use?
  • Before you start
• Running FastSurfer in a container
  • Using Apptainer (or Singularity)
  • Using Docker
  • FastSurfer flags in a container
  • Common problems
• Examples
  • Example 1: FastSurfer Apptainer (or Singularity)
  • Example 2: FastSurfer Docker
  • Example 3: Native FastSurfer on subjectX with parallel processing of hemis
  • Example 4: FastSurfer on multiple subjects
  • Example 5: Quick Segmentation
  • Example 6: Running FastSurfer on a SLURM cluster via Singularity
  • Example 7: Running FastSurfer with lesion inpainting using neurolit
• Output files
  • Segmentation module
  • Corpus Callosum module
  • CerebNet module
  • HypVINN module
  • Surface module
  • Lesion Inpainting Tool (LIT, optional)
  • Longitudinal Processing
• Modules
• Manual Edits
  • What are Edits?
  • What can be edited?
  • Pipeline overview
  • Possible Edits
  • General process
  • Bias field correction
  • asegdkt_segfile
  • Corpus callosum segmentation
  • Talairach registration
  • White matter segmentation
  • Pial surface placement
  • Side effects of edits
  • Guide for experienced FreeSurfer users
  • What NOT to do
• Longitudinal Processing
  • What is Longitudinal Processing?
  • How to Run Your Data
  • Single Time Point Cases
  • Running Individual Stages
  • Behind the Scenes
  • Final Statistics
  • References
• Reproducibility
  • On one machine
  • With a different thread count
  • Across machines
  • Checking a run
• Security Policy
  • Supported Versions
  • Reporting a Vulnerability
• FastSurfer License
  • Apache License
  • Other Packages and Tools distributed or used with FastSurfer