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Slicer FreeSurfer Commands

Key Investigators

• Ben Zwick (The University of Western Australia, Australia)
• Andy Huynh (The University of Western Australia, Australia)
• Steve Pieper (Isomics, Inc., USA)

Presenter location: In-person

Project Description

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

For example:

• mri_watershed - strip skull and other outer non-brain tissue:

  mri_watershed -brainsurf surface.vtk mri-t1.mgz stripped.mgz
  

  Note that FreeSurfer uses mgz file format.

• SynthStrip: Skull-Stripping for Any Brain Image implemented as FreeSurferSynthStripSkullStripScripted module:

  mri_synthstrip -i input -o stripped -m mask --no-csf
  

• SynthSeg: Segmentation of brain MRI scans implemented as FreeSurferSynthSeg module:

  mri_synthseg --i <input> --o <output> [--parc --robust --fast --vol <vol> --qc <qc> --post <post> --resample <resample> --crop <crop> --threads <threads> --cpu --v1 --ct]
  

  Note that SynthSeg is a Python package that can be installed without FreeSurfer.

Objective

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

Progress

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:
   • https://github.com/Slicer/ExtensionsIndex/pull/1943
   • https://github.com/PerkLab/SlicerFreeSurfer/issues/15

Illustrations

FreeSurfer SynthStrip Skull Strip

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:

• SlicerFreeSurfer
• SlicerNeuroSegmentation