BrainPrint represents a set of shape descriptors of a collection of subcortical and cortical structures. Note, that we moved most of this functionality to a pure python package: https://github.com/Deep-MI/BrainPrint-python The new package drops the shapeDNA-* and meshfix, Gmsh dependencies. ShapeDNA-tria functionality has mainly been replaced via our LaPy packages https://github.com/Deep-MI/LaPy The new python version, however, currently lacks support for 3D tetmeshes, as well as support for additional cortical regions and labels, which is why we will keep this package around as a legacy version.
- FreeSurfer (MRI data needs to be processed with Freesurfer 5.3 or newer): http://freesurfer.net
- shapeDNA-tria (to perform the shape analysis): http://reuter.mit.edu/software/shapedna
To also compute shape descriptors of 3D tetrahedra meshes, you additionally need:
- meshfix 1.2-alpha: https://code.google.com/p/meshfix/
- Gmsh: http://geuz.org/gmsh/
- shapeDNA-tetra (currently unavailable, contact author http://reuter.mit.edu/software/shapedna ) These are not required for the software to work, and only add 4 more descriptors for white and pial volumes (each hemisphere).
Set the environment variable $SHAPEDNA_HOME to the directory containing shapeDNA-tria. If you want to perform also 3D tetra processing, also copy gmsh, meshfix and shapeDNA-tetra to that directory. Source your FreeSurfer (5.3 or newer) and you are ready to go.
If you use this software for a publication please cite both these papers:
[1] BrainPrint: a discriminative characterization of brain morphology. Wachinger C, Golland P, Kremen W, Fischl B, Reuter M Neuroimage. 2015;109:232-48. http://dx.doi.org/10.1016/j.neuroimage.2015.01.032 http://www.ncbi.nlm.nih.gov/pubmed/25613439
[2] Laplace-Beltrami spectra as 'Shape-DNA' of surfaces and solids. Reuter M, Wolter F-E, Peinecke N Computer-Aided Design. 2006;38(4):342-366. http://dx.doi.org/10.1016/j.cad.2005.10.011
[1] contains the definition of the BrainPrint ensemble and neuroimaging application, while [2] introduces the shape descriptor (shapeDNA).
Homepage: http://reuter.mit.edu/software/brainprint
Author: Martin Reuter