Command Reference

All options of FastSurfer’s commands: run_fastsurfer.sh and its wrappers for longitudinal, batch, SLURM and BIDS processing, the scripts that run a single module directly, utilities, and the scripts for training the networks. To get started, see the User Guide.

• run_fastsurfer.sh
  • Required arguments
  • Optional arguments
  • Reproducibility
  • Troubleshooting
  • Full list of flags
• long_fastsurfer.sh
  • Usage help text
• brun_fastsurfer.sh
  • Usage
  • Subjects Lists
  • Parallelization with brun_fastsurfer.sh
  • Questions
• srun_fastsurfer.sh
  • Usage
  • Debugging SLURM runs
• bids_fastsurfer.py
  • Usage
  • Basic example
  • In Docker
  • Output naming
  • Sessions
  • T1w and T2w input
  • Validation
  • Dry run
• Running modules directly
  • FastSurferCNN: run_prediction.py
  • CerebNet: run_prediction.py
  • HypVINN: run_prediction.py
  • CorpusCallosum: fastsurfer_cc.py
  • Surface pipeline: recon-surf.sh
  • Surface registration: recon-surfreg.sh
• Utilities
  • FastSurferCNN: download_checkpoints.py
  • FastSurferCNN: conform.py
  • FastSurferCNN: segstats.py
  • tools: compare_subjects.py
  • CorpusCallosum: cc_visualization.py
  • recon_surf: long_compat_segmentHA.py
• Training
  • FastSurferCNN: generate_hdf5.py
  • FastSurferCNN: run_model.py