ABLE: Automated Brain Lines Extraction Based on Laplacian Skeletonization

Work in Progress

This MATLAB tool takes brain MR images processed with FreeSurfer (?h.white, ?h.pial, ?h.curv, ?h.curv.pial, and ?h.aparc.annot) and extracts gyral crown and sulcal fundi lines in the given mesh as pairs of connected vertices in the surface.

Usage

The process can be invoked using

Launch_Morph_Processing(pialSurfLHFile, pialCurvLHFile, whiteSurfLHFile, whiteCurvLHFile, annotLHFile, pialSurfRHFile, pialCurvRHFile, whiteSurfRHFile, whiteCurvRHFile, annotRHFile, outputFile)

The output is a MATLAB structure containing the lines, depth map, sulcal basins used for the segmentation, and endpoints obtained for both right and left hemispheres of the given subject.

Installation

First clone the repository with

git clone --recursive https://github.com/albertofpena/ABLE.git

Then, gptoolbox must be compiled, for that

cd ABLE/dependencies/gptoolbox/mex
mkdir build
cd build
cmake ..
make

Further instructions can be found in https://github.com/alecjacobson/gptoolbox/blob/master/mex/README.md

Finally, just add the dependencies folder to the MATLAB path.

Citation

If you use this code, please cite the paper in https://doi.org/10.1007/s12021-022-09601-7