TTFields-Workflow

An SPM8 toolbox for automating MRIs to FEA models for TTFields

Takes a DICOM MRI directory as input and outpus binarized image masks for use in FEA mesh generation.

A more complete background and characterization of the workflow can be found at: Timmons, J.J. et al 2017 Phys. Med. Biol. 62 8264.

Installation and use

1. Download the repo (Clone or download > Download ZIP) and unzip into SPM8/toolbox (or elsewhere)
2. In MATLAB, add the SPM8 path
3. Add the path and subpaths of TTFields-Workflow
4. Type and enter "TTFs" in the MATLAB console
5. Within the prompt, navigate to a DICOM directory for segmentation and select all images; ctrl-A then Enter then click "Done"

addpath('C:\spm8')

addpath(genpath('C:\spm8\toolbox\TTfields-Workflow-master'))

TTFs

Optional function calls

pyScanIPScript and batScript, uncommented, can be used to generate ScanIP post-processing and initialization scripts, respectively. We use them for speed/convenience

Dependencies

Most dependencies have been included, but they are listed below along with their sources

MATLAB Image Processing Toolbox

Required but not included. Please see Mathworks.com

Huang et al., 2013

Y. Huang, J.P. Dmochowski, Y. Su, A. Datta, C. Rorden, L.C. Parra, Automated MRI Segmentation for Individualized Modeling of Current Flow in the Human Head, Journal of Neural Engineering, 10(6):066004, 2013.

NIfTI_tools

Tools for NIfTI and ANALYZE image by Jimmy Shen

cylinder2P

Cylinder generation function by Wei Pan

knnsearch

k-nearest neighbors search by Yi Cao

normnd

normal vector algo by Jered Wells