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SlicerCBM: Computational Biophysics for Medicine in 3D Slicer

Key Investigators

• Benjamin Zwick (The University of Western Australia)
• Saima Safdar (The University of Western Australia)
• Andy Huynh (The University of Western Australia)
• Gerry Gralton (The University of Western Australia)
• Adam Wittek (The University of Western Australia)
• Karol Miller (The University of Western Australia)

Project Description

SlicerCBM is an extension for 3D Slicer that provides tools for creating and solving computational models of biophysical systems and processes with a focus on clinical and biomedical applications.

Objective

1. Package SlicerCBM modules as an installable 3D Slicer extension.

2. Improve documentation of individual modules and workflow.

Approach and Plan

1. Complete the requirements for a new 3D Slicer extension (https://github.com/SlicerCBM/SlicerCBM/issues/8)

2. Add the SlicerCBM extension to the Slicer Extensions Catalog.

Progress and Next Steps

1. Individual modules have been developed and are available on GitHub (https://github.com/SlicerCBM/SlicerCBM)

2. Checklist for submitting a new extension (https://github.com/SlicerCBM/SlicerCBM/issues/8)

Illustrations

Background and References

Code repository and documentation:

• https://github.com/SlicerCBM/SlicerCBM
• https://slicercbm.github.io/

Sample data:

• Zwick BF, Safdar S, Bourantas GC, Joldes GR, Hyde DE, Warfield SK, Wittek A, Miller K. Data for patient-specific solution of the electrocorticography forward problem in deforming brain [Data set]. Zenodo; 2022. https://doi.org/10.5281/zenodo.7309089

Publications:

• Safdar S, Zwick BF, Bourantas G, Joldes GR, Warfield SK, Hyde DE, Wittek A, Miller K. Automatic Framework for Patient-Specific Biomechanical Computations of Organ Deformation: An Epilepsy (EEG) Case Study. In: Nielsen PMF, Nash MP, Li X, Miller K, Wittek A, editors. Computational Biomechanics for Medicine. Cham: Springer International Publishing; 2022. p. 75–89.

• Zwick BF, Bourantas GC, Safdar S, Joldes GR, Hyde DE, Warfield SK, Wittek A, Miller K. Patient-specific solution of the electrocorticography forward problem in deforming brain. NeuroImage. 2022;263:119649.

• Yu Y, Safdar S, Bourantas GC, Zwick BF, Joldes GR, Kapur T, Frisken S, Kikinis R, Nabavi A, Golby A, Wittek A, Miller K. Automatic framework for patient-specific modelling of tumour resection-induced brain shift. Comput Biol Med. 2022;143:105271.

• Safdar S, Joldes GR, Zwick BF, Bourantas GC, Kikinis R, Wittek A, Miller K. Automatic Framework for Patient-Specific Biomechanical Computations of Organ Deformation. In: Miller K, Wittek A, Nash M, Nielsen PMF, editors. Computational Biomechanics for Medicine. Cham: Springer; 2021. p. 3–16.