Computer-assisted brain surgery planning
Python 3, git, pip3.
Follow instructions to install pathfinder.
Install CGAL.
sudo install libcgal-dev
git clone https://github.com/myociss/freesurgery
pip3 install ./freesurgery
To obtain a mesh and color map from a subject file: freesurgery_mri2mesh3d subject_file.nii facet_size
$ freesurgery_mri2mesh3d aparc_aseg.nii.gz small
To obtain a mesh from a subject file using FreeSurfer's color lookup table:
$ freesurgery_mri2mesh3d aparc_aseg.nii.gz small $FREESURFER_HOME/FreeSurferColorLUT.txt
To assign weights to a mesh and convert it to pathfinder's expected format: freesurgery_mesh2json mesh_file.mesh weights_file.txt
$ freesurgery_mesh2json aparc_aseg.mesh weights.txt
To generate a list of paths: freesurgery_generate_paths mesh_json.json target planes_to_search width_bound
$ freesurgery_generate_paths aparc_aseg.json “100,100,150” 16 0.01
To view a mesh with paths: freesurgery_view_mesh mesh_json.json color_map.txt paths.json
$ freesurgery_view_mesh aparc_aseg.json aparc_aseg_colors.txt aparc_aseg_paths.json