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.
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.
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.
There is a Docker available that can be used with the following command:
docker run -v /path/to/freesurfer/subject/:/input -v /path/to/output/folder:/out albertofpena/able:latest ABLE /input /out/subj.mat
Note that in this case, the initial depth map is estimated using a travel depth algorithm instead of the exact geodesic.
If you use this code, please cite the paper in https://doi.org/10.1007/s12021-022-09601-7