Python bindings for ROBEX brain extraction.
This package comes with ROBEX v1.2 for Linux. Windows is not currently supported.
- Free software: BSD license
- Documentation: https://pyrobex.readthedocs.io.
The easiest way to install the package is with:
pip install pyrobex
Alternatively, you can download the source and run:
python setup.py install
This package provides a CLI (to the CLI) of ROBEX for convenience and testing which can be accessed through, e.g.,:
robex path/to/t1w_image.nii -os path/to/stripped.nii -om path/to/mask.nii
The real use-case of this package is by importing robex and using it within another script or neuroimaging pipeline, e.g.,
import nibabel as nib
from pyrobex.robex import robex
image = nib.load('path/to/t1w_image.nii')
stripped, mask = robex(image)If you use this package in support of an academic publication, please cite:
@article{iglesias2011robust,
title={Robust brain extraction across datasets and comparison with publicly available methods},
author={Iglesias, Juan Eugenio and Liu, Cheng-Yi and Thompson, Paul M and Tu, Zhuowen},
journal={IEEE transactions on medical imaging},
volume={30},
number={9},
pages={1617--1634},
year={2011},
publisher={IEEE}
}