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pyrobex

Documentation Status

Python bindings for ROBEX brain extraction.

This package comes with ROBEX v1.2 for Linux. Windows is not currently supported.

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}
}