semvec/pypi-packages huggingface dataset:
pyrobex 0.4.3
python bindings for ROBEX brain extraction
License: BSD license
Requires Python: >=3.7
Keywords: robex,brain extraction,mri

=======
pyrobex
=======

.. image:: https://img.shields.io/pypi/v/pyrobex.svg
        :target: https://pypi.python.org/pypi/pyrobex

.. image:: https://anaconda.org/conda-forge/pyrobex/badges/version.svg
        :target: https://anaconda.org/conda-forge/pyrobex
        
.. image:: https://api.travis-ci.com/jcreinhold/pyrobex.svg
        :target: https://travis-ci.com/github/jcreinhold/pyrobex

.. image:: https://readthedocs.org/projects/pyrobex/badge/?version=latest
        :target: https://pyrobex.readthedocs.io/en/latest/?version=latest
        :alt: Documentation Status


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.,

.. code-block:: python

    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}
    }

.. _ROBEX: https://www.nitrc.org/projects/robex


=======
History
=======

0.4.2 (2021-05-25)
------------------

* Use black code style and add tests, docs.

0.4.1 (2021-05-06)
------------------

* Improve logging.

0.4.0 (2021-05-06)
------------------

* Fix logging in CLI.

0.3.0 (2021-05-06)
------------------

* Fix to antspy backend.

0.2.0 (2021-05-06)
------------------

* Fixes the distribution of ROBEX on PyPI.

0.1.0 (2021-05-05)
------------------

* First release on PyPI.