README.md

Slicer FreeSurfer Commands

Run FreeSurfer commands using 3D Slicer's graphical user interface.

Features include:

• segmentation (SynthSeg)
• skull stripping (SynthStrip)

Modules

The FreeSurfer Commands extension for 3D Slicer contains the following modules:

• (TODO) FreeSurfer MRI Watershed Skull Strip: Skull stripping using FreeSurfer's MRI watershed (FSW) algorithm through the mri_watershed command.

• FreeSurfer SynthSeg Brain MRI Segmentation: Brain MRI segmentation using SynthSeg packaged in FreeSurfer as the mri_synthseg command.

• FreeSurfer SynthStrip Skull Strip: Skull stripping using FreeSurfer's SynthStrip tool through the mri_synthstrip command.

Installation

You must have FreeSurfer (version 7.3.2 or higher) installed on your computer and have the $FREESURFER_HOME environment variable set correctly. Please refer to the FreeSurfer documentation for further details.

The FreeSurfer Commands extension for 3D Slicer has been tested on the following operating systems:

• Debian GNU/Linux 12 (bookworm) with 3D Slicer 5.2.2

Feature Requests

Please open an issue if you would like to suggest a new feature or FreeSurfer command to be added.

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.