Metadata-Version: 2.1
Name: cmb
Version: 0.0.6
Summary: Cere-MEG-Bellum (CMB) - Cerbellum segmentation and forward solution calculation
Home-page: https://github.com/johnsam7/ceremegbellum
Maintainer: John Gustaf Wilhelm Samuelsson
Maintainer-email: johnsam@mit.edu
License: MIT License
Download-URL: https://github.com/johnsam7/ceremegbellum
Project-URL: Source, https://github.com/johnsam7/ceremegbellum/
Project-URL: Tracker, https://github.com/johnsam7/ceremegbellum/issues/
Description: .. -*- mode: rst -*-
        
        |PyPI|_ |GH-CI|_
        
        .. |PyPI| image:: https://badge.fury.io/py/cmb.svg?label=PyPI%20downloads
        .. _PyPI: https://pypi.org/project/cmb/
        
        .. |GH-CI| image:: https://github.com/johnsam7/ceremegbellum/actions/workflows/ci.yml/badge.svg?branch=main
        .. _GH-CI: https://github.com/johnsam7/ceremegbellum/actions/workflows/ci.yml
        
        
        Cere-MEG-Bellum (CMB) Package
        =============================
        
        For more information about CMB, please read the following paper:
        
          Samuelsson J G , Rosen B, Hamalainen M S. *Automatic Reconstruction of Cerebellar Cortex from Standard MRI Using Diffeomorphic Registration of a High-Resolution Template (ARCUS).* bioRxiv 2020.11.30.405522; doi: https://doi.org/10.1101/2020.11.30.405522
        
        
        Installation
        ^^^^^^^^^^^^
        
        To install the latest stable version of CMB, you can use pip_ in a terminal:
        
        .. code-block:: bash
        
            pip install -U cmb
        
        
        Usage of the Docker Container
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        before building the image please place in this folder the freesurfer archive 'freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz' along with the freesurfer license file 'license.txt'.
        
        Subsequently build the docker image with
        
        .. code-block:: bash
        
            docker build -t mne-tools/cmb:v0.01 .
        
        and run it with
        
        .. code-block:: bash
        
            docker run -ti -v <YOUR SUBJECTS DIR>:/workspace/subjects -v <YOUR PROCESSED nnUNet DIR>:/workspace/nnUNet -v <YOUR ceremegbellum GIT DIR>:/workspace/ceremegbellum --name CMB mne-tools/cmb:v0.01
        
        It is convinient to install CMB for development directly from the local repository. Change the directory to to '/workspace/ceremegbellum' in the CLI of the Docker Container and run
        
        .. code-block:: bash
        
            pip install -e .
        
        
        Licensing
        ^^^^^^^^^
        CMB is **MIT-licensed**:
        
            Copyright (c) 2021-2022, authors of CMB.
            All rights reserved.
        
            Permission is hereby granted, free of charge, to any person obtaining a copy
            of this software and associated documentation files (the "Software"), to deal
            in the Software without restriction, including without limitation the rights
            to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
            copies of the Software, and to permit persons to whom the Software is
            furnished to do so, subject to the following conditions:
        
            The above copyright notice and this permission notice shall be included in all
            copies or substantial portions of the Software.
        
            **THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
            IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
            FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
            AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
            LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
            OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
            SOFTWARE.**
        
        
        .. _pip: https://pip.pypa.io/en/stable/
        
Keywords: neuroscience neuroimaging MEG cerebellum brain
Platform: any
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.7
Description-Content-Type: text/x-rst
