BrainPrint

This is the brainprint python package, a derivative of the original BrainPrint-legacy scripts, with the primary goal to provide a Python-only version (except some Freesurfer dependencies), to integrate the LaPy package, and to remove dependencies on third-party software (shapeDNA-* binaries, gmsh, meshfix). As a result, some functionality of the original BrainPrint-legacy scripts is no longer maintained (currently no support of tetrahedral meshes and no support of cortical parcellations or label files).

Usage

Usage from the command line

The toolbox consists of the brainprint.py Python script, which can be run from the command line as well as from within a Python environment.

The brainprint.py script is used for the per-subject computation of the individual brainprint descriptor. Its usage and options are summarized below; detailed info is available by calling the script without any arguments from the command line.

python3 brainprint.py --sdir <directory> --sid <SubjectID>  [--num <num>]
                    [--evec] [--skipcortex] [--norm <surface|volume|geometry|none> ]
                    [--reweight] [--asymmetry] [--outdir <directory>] [--help]
                    [--more-help]

Options:
  --help           Show this help message and exit
  --more-help      Show extensive help message and exit

Required options:
  --sid <SubjectID>
                   Subject ID (FreeSurfer-processed directory inside the
                   subjects directory)
  --sdir <directory>
                   FreeSurfer subjects directory

Processing directives:
  --num <num>      Number of eigenvalues/vectors to compute (default: 50)
  --evec           Switch on eigenvector computation (default: off)
  --skipcortex     Skip cortical surfaces (default: off)
  --norm <surface|volume|geometry|none>
                   Switch on eigenvalue normalization; will be either surface,
                   volume, or determined by the geometry of the object. Use
                   "none" or leave out entirely to skip normalization.
  --reweight       Switch on eigenvalue reweighting (default: off)
  --asymmetry      Perform left-right asymmetry calculation (default: off)

Output parameters:
  --outdir=OUTDIR  Output directory (default: <sdir>/<sid>/brainprint)

Usage as a Python package

As an alternative to their command-line usage, the BrainPrint scripts can also be run within a pure Python environment, i.e. installed and imported as a Python package.

Use import brainprint (or sth. equivalent) to import the package within a Python environment.

Use the run_brainprint function from the brainprint module to run an analysis:

import lapy
from brainprint import brainprint
brainprint.run_brainprint(sdir="/my/subjects/directory", sid="my_subject_id")

Additional options are num=<int>, evec=<bool>, skipcortex=<bool>, norm=<"surface"|"volume"|"geometry"|"none">, reweight=<bool>, and outdir=<string>.

See help(brainprint) and brainprint.get_help() for further usage info and additional options.

Output

The script will create an output directory that contains a csv table with values (in that order) for the area, volume, and first n eigenvalues per each FreeSurfer structure. An additional output file will be created if the asymmetry calculation is performed.

Installation

Use the following code to download, build and install a package from this repository into your local Python package directory:

pip3 install --user git+https://github.com/Deep-MI/BrainPrint-python.git

This will also install the necessary dependencies, e.g. the LaPy package. You may need to add your local Python package directory to your $PATH in order to run the scripts.

Requirements

The LaPy package must be installed.
A working installation of Freesurfer 6.0 must be sourced.
At least one structural MR image that was processed with Freesurfer 6.0.

Changes

There are some changes in functionality in comparison to the original BrainPrint scripts:

currently no support for tetrahedral meshes
currently no support for analyses of cortical parcellation or label files
no more Python 2.x compatibility

References

If you use this software for a publication please cite:

[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;38:342-366. http://dx.doi.org/10.1016/j.cad.2005.10.011

af-a / BrainPrint-python