fastsurfer

Module: segmentation/fastsurfer

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Inputs

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	true
anat	file	An anatomy (ex, .nii.gz).		*.{nii,nii.gz,mgz}
fs_license	file	The path to your FreeSurfer license. To get one, go to https://surfer.nmr.mgh.harvard.edu/registration.html. Optional. If you have already set your license as prescribed by Freesurfer (copied to a .license file in your $FREESURFER_HOME), this is not required.		*.txt

Arguments

	Type	Description	Choices	Default
acq3T	boolean	Use this flag if the input T1w image was acquired at 3T.		False
cerebnet	boolean	Use this flag to enable cerebellum sub-segmentation with CerebNet.		False
hypvinn	boolean	Use this flag to enable hypothalamus sub-segmentation with HypVinn.		False
seg_only	boolean	Use this flag to only run the segmentation part of FastSurfer. If false, will also run the surface reconstruction part (recon-surf).		True

Outputs

	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
fastsurferdirectory	file	Sorted BAM/CRAM/SAM file	*.{bam,cram,sam}
versions	file	File containing software versions	versions.yml

Tools

	Description	Homepage	DOI
Fastsurfer	The FastSurfer pipeline consists of two main parts for segmentation and surface reconstruction.	https://github.com/Deep-MI/FastSurfer

Authors

@arnaudbore

Maintainers

@arnaudbore