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Slicer FreeSurfer Commands
Presenter location: In-person
- Ben Zwick (The University of Western Australia, Australia)
- Andy Huynh (The University of Western Australia, Australia)
- Steve Pieper (Isomics, Inc., USA)
SlicerFreeSurferCommands aims to provide a graphical user interface for running FreeSurfer commands within 3D Slicer.
- Complete the development of existing modules based on Slicer user and developer feedback.
- Develop additional modules for other commands (e.g. SynthSeg).
- Package modules as an installable 3D Slicer extension.
Approach and Plan
- Demonstrate and get feedback on the use and implementation of the existing modules from Slicer users and developers.
- Discuss the implementation of the modules with Slicer developers (in particular the use of CLI vs scripted Python modules for this application).
- Modify modules based on feedback from Slicer developers.
- Complete the new extension checklist.
Progress and Next Steps
- Developed Python scripted module (and CLI module which is now deprecated) for FreeSurfer’s SynthStrip command for skull stripping.
- Developed Python scripted module for FreeSurfer’s SynthSeg Brain MRI Segmentation command.
- Completed the new extension checklist.
- Discuss merging SlicerFreeSurfer and SlicerFreeSurferCommands, and moving to Slicer GitHub organization. See:
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: