Modules

run_fastsurfer.sh runs FastSurfer’s modules one after the other: first the segmentation modules, which take a few minutes on a GPU, then the surface reconstruction, which takes about an hour. All modules run by default; each page describes what a module computes, what it needs, how to switch it off or adjust it, and how to cite it.

Segmentation modules:

• Whole-brain segmentation (FastSurferVINN), the core module the others build on

• Corpus callosum (FastSurfer-CC)

• Cerebellum sub-segmentation (CerebNet)

• Hypothalamus sub-segmentation (HypVINN)

Surface module:

• Surface reconstruction (recon-surf)

Extension:

• Lesion inpainting (LIT), for images with large lesions