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, 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 As a result, some functionality of the original BrainPrint-legacy scripts is no longer maintained (currently no support of tetrahedral meshes and no support of cortical parcellations or label files).

Installation¶

Use the following code to install the latest release of LaPy into your local Python package directory:

python3 -m pip install brainprint

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.

Usage¶

Command Line Interface (CLI)¶

Once installed, the package provides a brainprint executable which can be run from the command line.

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

brainprint Command-Line Interface¶

brainprint
--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).

--cholmod Switch on use of (faster) Cholesky decomposition instead of (slower) LU decomposition (default: off). May require manual install of scikit-sparse package.

Output parameters¶

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

--keep-temp Whether to keep the temporary files directory or not (default: False).

Python Package¶

brainprint can also be run within a pure Python environment, i.e. installed and imported as a Python package. E.g.:

from brainprint import Brainprint

subjects_dir = "/path/to/freesurfer/subjects_dir/"
subject_id = "42"

bp = Brainprint(subjects_dir=subjects_dir, asymmetry=True, keep_eigenvectors=True)
results = bp.run(subject_id=subject_id)
results
{"eigenvalues": PosixPath("/path/to/freesurfer/subjects_dir/subject_id/brainprint/subject_id.brainprint.csv"),
"eigenvectors": PosixPath("/path/to/freesurfer/subjects_dir/subject_id/brainprint/eigenvectors"),
"distances": PosixPath("/path/to/freesurfer/subjects_dir/subject_id/brainprint/subject_id.brainprint.asymmetry.csv")}

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 and/or for the eigenvectors (CLI --evecs flag or keep_eigenvectors on class initialization).

Changes¶

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

Currently, there is no support for tetrahedral meshes.
Currently, there is 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 PubMed

[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