segmentation_fastsurfer
Perform whole brain segmentation and surface reconstruction using deep-learning through FastSurfer.
Keywords : segmentation, fastsurfer, deepmi, cnn, deep-learning
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(anat), path(fs_license)
| 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). | True | *.{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. | True | *.txt |
Outputs
Section titled “Outputs”fastsurferdirectory
Section titled “fastsurferdirectory”Format : tuple val(meta), path(*_fastsurfer)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | True | |
| *_fastsurfer | directory | Fastsurfer segmentation outputs. | True | *_fastsurfer |
versions
Section titled “versions”Format : path(versions.yml)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| versions.yml | file | File containing software versions | True | versions.yml |
Arguments (see process.ext)
Section titled “Arguments (see process.ext)”| Type | Description | Default | Choices | |
|---|---|---|---|---|
| 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 | |
| single_thread | boolean | If true, the command will be run in single-threaded mode. By default, the command will use multiple threads based on the number of CPUs allocated to the task. | False |
| Description | DOI | |
|---|---|---|
| Fastsurfer | The FastSurfer pipeline consists of two main parts for segmentation and surface reconstruction. |
Authors
Section titled “Authors”Last updated : 2026-05-12