segmentation_fsreconall
Performs Freesurfer’s recon-all script to segment your anatomy (probably a T1) into labels, surfaces, and much more. See the full documentation here: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all.
Keywords : neural network, Artificial intelligence, machine learning, Segmentation, Tissues
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:'test', 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”recon_all_out_folder
Section titled “recon_all_out_folder”Format : tuple val(meta), path(*__recon_all)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__recon_all | directory | Directory containing all recon-all outputs. | True | *__recon_all |
versions
Section titled “versions”Format : path(versions.yml)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| versions.yml | file | File containing software versions | True | versions.yml |
| Description | DOI | |
|---|---|---|
| Freesurfer | Open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images. | 10.1016/j.neuroimage.2012.01.021 |
Authors
Section titled “Authors”Last updated : 2025-10-30