Edit this page

NA-MIC Project Weeks

Back to Projects List

Slicer FreeSurfer Commands

Key Investigators

Presenter location: In-person

Project Description

SlicerFreeSurferCommands aims to provide a graphical user interface for running FreeSurfer commands within 3D Slicer.

For example:


  1. Complete the development of existing modules based on Slicer user and developer feedback.
  2. Develop additional modules for other commands (e.g. SynthSeg).
  3. Package modules as an installable 3D Slicer extension.

Approach and Plan

  1. Demonstrate and get feedback on the use and implementation of the existing modules from Slicer users and developers.
  2. Discuss the implementation of the modules with Slicer developers (in particular the use of CLI vs scripted Python modules for this application).
  3. Modify modules based on feedback from Slicer developers.
  4. Complete the new extension checklist.

Progress and Next Steps


  1. Developed Python scripted module (and CLI module which is now deprecated) for FreeSurfer’s SynthStrip command for skull stripping.
  2. Developed Python scripted module for FreeSurfer’s SynthSeg Brain MRI Segmentation command.
  3. Completed the new extension checklist.

Next steps

  1. Discuss merging SlicerFreeSurfer and SlicerFreeSurferCommands, and moving to Slicer GitHub organization. See:


FreeSurfer SynthStrip Skull Strip FreeSurfer SynthStrip Skull Strip

FreeSurfer SynthSeg Brain MRI Segmentation FreeSurfer SynthSeg Brain MRI Segmentation

Background and References

Software repository: https://github.com/SlicerCBM/SlicerFreeSurferCommands

FreeSurfer website: https://freesurfer.net/

Similar extensions for 3D Slicer: