pyrobex

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.

Install

The easiest way to install the package is with:

pip install pyrobex

Alternatively, you can download the source and run:

python setup.py install

Basic Usage

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)

References

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}
}