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original BrainPrint-legacy scripts is no longer maintained (currently no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