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mne-connectivity

Connectivity algorithms that leverage the MNE-Python API.

https://github.com/mne-tools/mne-connectivity

Science Score: 64.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: pubmed.ncbi, ncbi.nlm.nih.gov
  • ✓
    Committers with academic emails
    1 of 21 committers (4.8%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.5%) to scientific vocabulary

Keywords

connectivity dynamics mne-python statistics

Keywords from Contributors

bids neuroimaging meg eeg magnetoencephalography electroencephalography neuroscience ieeg electrocorticography ecog
Last synced: 6 months ago · JSON representation ·

Repository

Connectivity algorithms that leverage the MNE-Python API.

Basic Info
Statistics
  • Stars: 82
  • Watchers: 12
  • Forks: 38
  • Open Issues: 61
  • Releases: 7
Topics
connectivity dynamics mne-python statistics
Created almost 5 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Citation

README.rst 

.. -*- mode: rst -*-

|GH|_ |Circle|_ |Azure|_ |Codecov|_ |PyPI|_ |PyPI_Release|_ |conda-forge|_ 

.. |GH| image:: https://github.com/mne-tools/mne-connectivity/actions/workflows/unit_tests.yml/badge.svg
.. _GH: https://github.com/mne-tools/mne-connectivity/actions/workflows/unit_tests.yml

.. |Circle| image:: https://circleci.com/gh/mne-tools/mne-connectivity.svg?style=shield
.. _Circle: https://circleci.com/gh/mne-tools/mne-connectivity

.. |Azure| image:: https://dev.azure.com/mne-tools/mne-connectivity/_apis/build/status/mne-tools.mne-connectivity?branchName=main
.. _Azure: https://dev.azure.com/mne-tools/mne-connectivity/_build/latest?definitionId=1&branchName=main

.. |Codecov| image:: https://codecov.io/gh/mne-tools/mne-connectivity/branch/main/graph/badge.svg
.. _Codecov: https://codecov.io/gh/mne-tools/mne-connectivity

.. |conda-forge| image:: https://img.shields.io/conda/dn/conda-forge/mne-connectivity.svg?label=Conda%20downloads
.. _conda-forge: https://anaconda.org/conda-forge/mne-connectivity

.. |PyPI| image:: https://img.shields.io/pypi/dm/mne-connectivity.svg?label=PyPI%20downloads
.. _PyPI: https://pypi.org/project/mne-connectivity/

.. |PyPI_Release| image:: https://img.shields.io/pypi/v/mne-connectivity.svg
.. _PyPI_Release: https://pypi.org/project/mne-connectivity/

.. _MNE-Connectivity: https://mne.tools/mne-connectivity/dev/
.. _MNE-Python: https://mne.tools/stable
.. _MNE-Connectivity documentation: https://mne.tools/mne-connectivity/stable/index.html
.. _installation guide: https://mne.tools/mne-connectivity/dev/install/index.html
.. _pip: https://pip.pypa.io/en/stable/
.. _Frites: https://github.com/brainets/frites
.. _contributing guide: https://github.com/mne-tools/mne-connectivity/blob/main/CONTRIBUTING.md

MNE-Connectivity
================

`MNE-Connectivity`_ is an open-source Python package for connectivity and
related measures of MEG, EEG, or iEEG data built on top of the 
`MNE-Python`_ API. It includes modules for data input/output, visualization,
common connectivity analysis, and post-hoc statistics and processing.


.. target for :end-before: title-end-content

This project was initially ported over from mne-python starting v0.23, by Adam
Li as part of Google Summer of Code 2021. Subsequently v0.1 and v0.2 releases
were done as part of GSoC period. Future development will occur in subsequent
versions. 

Documentation
^^^^^^^^^^^^^

Stable `MNE-Connectivity documentation`_ is available online.

Installing MNE-Connectivity
^^^^^^^^^^^^^^^^^^^^^^^^^^^

To install the latest stable version of MNE-Connectivity, you can use pip_ in a terminal:

.. code-block:: bash

    pip install -U mne-connectivity

For more complete instructions and more advanced installation methods (e.g. for
the latest development version), see the `installation guide`_.


Get the latest code
^^^^^^^^^^^^^^^^^^^

To install the latest version of the code using pip_ open a terminal and type:

.. code-block:: bash

    pip install -U https://github.com/mne-tools/mne-connectivity/archive/main.zip

To get the latest code using `git `__, open a terminal and type:

.. code-block:: bash

    git clone https://github.com/mne-tools/mne-connectivity.git

Alternatively, you can also download a
`zip file of the latest development version `__.


Contributing to MNE-Connectivity
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Please see the documentation on the MNE-Connectivity homepage:

https://github.com/mne-tools/mne-connectivity/blob/main/CONTRIBUTING.md


Forum
^^^^^^

https://mne.discourse.group

A Note About Connectivity
^^^^^^^^^^^^^^^^^^^^^^^^^

In the neuroscience community as of 2021, the term "functional connectivity" can 
have many different meanings and comprises many different measures. Some of 
these measures are directed (i.e. try to map a statistical causal relationship between
brain regions), others are non-directed. Please note that the interpretation of your 
functional connectivity measure depends on the data and underlying
assumptions. 
For a taxonomy of functional connectivity measures and information on the 
interpretation of those measures, we refer to
`Bastos and Schoffelen`_.

In mne-connectivity, we do not claim that any of our measures imply causal
connectivity.

.. _Bastos and Schoffelen: https://pubmed.ncbi.nlm.nih.gov/26778976/

Owner

  • Name: MNE tools for MEG and EEG data analysis
  • Login: mne-tools
  • Kind: organization

Citation (CITATION.cff) 

# Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
cff-version: 1.1.0
message: "If you use this software, please cite it using the metadata below."
authors:
  - given-names: "Adam"
    family-names: "Li"
    orcid: https://orcid.org/0000-0001-8421-365X
  - given-names: "Daniel"
    family-names: "McCloy"
    orcid: https://orcid.org/0000-0002-7572-3241
  - given-names: "Eric"
    family-names: "Larson"
    orcid: https://orcid.org/0000-0003-4782-5360
  - given-names: "Britta"
    family-names: "Westner"
    orcid: https://orcid.org/0000-0003-3231-1076
  - given-names: "Alexander"
    family-names: "Kroner"
    orcid: https://orcid.org/0000-0001-8139-0095
  - given-names: "Alexandre"
    family-names: "Gramfort"
    orcid: https://orcid.org/0000-0001-9791-4404
  - given-names: "Thomas Samuel"
    family-names: "Binns"
    orcid: https://orcid.org/0000-0003-0657-0891
  - given-names: "Mohammad"
    family-names: "Orabe"
    orcid: https://orcid.org/0009-0004-7177-799X


title: "mne-connectivity"
version: 0.6.0
date-released: 2024-12-06
url: "https://github.com/mne-tools/mne-connectivity"

GitHub Events

Total
  • Issues event: 32
  • Watch event: 11
  • Delete event: 28
  • Issue comment event: 136
  • Push event: 105
  • Pull request review event: 92
  • Pull request review comment event: 208
  • Pull request event: 86
  • Fork event: 2
  • Create event: 33
Last Year
  • Issues event: 32
  • Watch event: 11
  • Delete event: 28
  • Issue comment event: 136
  • Push event: 105
  • Pull request review event: 92
  • Pull request review comment event: 208
  • Pull request event: 86
  • Fork event: 2
  • Create event: 33

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 273
  • Total Committers: 21
  • Avg Commits per committer: 13.0
  • Development Distribution Score (DDS): 0.718
Past Year
  • Commits: 68
  • Committers: 5
  • Avg Commits per committer: 13.6
  • Development Distribution Score (DDS): 0.368
Top Committers
Name Email Commits
Thomas Samuel Binns t****s@o****m 77
Adam Li a****2@g****m 59
pre-commit-ci[bot] 6****] 49
Eric Larson l****d@g****m 19
Adam Li a****2@A****l 13
Daniel McCloy d****n@m****o 11
Alex a****l@m****g 10
Adam Li a****2@a****n 9
Adam Li a****2@n****e 6
dependabot[bot] 4****] 5
Adam Li a****2@A****e 3
Santeri Ruuskanen 6****s 2
Qianliang Li 3****e 2
Jonathan Shor 1****r 1
Alexander Kroner a****r@m****l 1
Kenji Marshall k****9@g****m 1
Mohammad 4****e 1
Moritz Gerster 4****r 1
Richard M. Köhler r****r@o****e 1
Sam Steingold s****s@g****g 1
SezanMert 7****t 1
Committer Domains (Top 20 + Academic)
gnu.org: 1 outlook.de: 1 maastrichtuniversity.nl: 1 adams-mbp-2.home: 1 new-host-2.home: 1 adams-mbp-2.lan: 1 mailbox.org: 1 mccloy.info: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 101
  • Total pull requests: 260
  • Average time to close issues: 4 months
  • Average time to close pull requests: 9 days
  • Total issue authors: 36
  • Total pull request authors: 23
  • Average comments per issue: 3.77
  • Average comments per pull request: 2.49
  • Merged pull requests: 225
  • Bot issues: 0
  • Bot pull requests: 105
Past Year
  • Issues: 25
  • Pull requests: 106
  • Average time to close issues: 22 days
  • Average time to close pull requests: 6 days
  • Issue authors: 9
  • Pull request authors: 7
  • Average comments per issue: 1.84
  • Average comments per pull request: 0.85
  • Merged pull requests: 92
  • Bot issues: 0
  • Bot pull requests: 76
View more stats
Top Authors
Issue Authors
  • adam2392 (26)
  • tsbinns (24)
  • drammock (6)
  • JohannesWiesner (6)
  • hoechenberger (3)
  • Div12345 (3)
  • agramfort (2)
  • seqasim (2)
  • ruuskas (2)
  • larsoner (1)
  • alexanderkroner (1)
  • witherscp (1)
  • Sirabhop (1)
  • max-hill-4 (1)
  • mscheltienne (1)
Pull Request Authors
  • pre-commit-ci[bot] (94)
  • tsbinns (72)
  • adam2392 (27)
  • drammock (15)
  • larsoner (15)
  • dependabot[bot] (11)
  • ruuskas (4)
  • alexrockhill (3)
  • Avoide (3)
  • richardkoehler (2)
  • seqasim (2)
  • moritz-gerster (1)
  • alexanderkroner (1)
  • sam-s (1)
  • kenjimarshall (1)
Top Labels
Issue Labels
good first issue (6) help wanted (6) enhancement (5) documentation (3) bug (2)
Pull Request Labels
dependencies (11) Needs Discussion (1) github_actions (1) bug (1)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 18,443 last-month
  • Total dependent packages: 6
    (may contain duplicates)
  • Total dependent repositories: 4
    (may contain duplicates)
  • Total versions: 10
  • Total maintainers: 2
pypi.org: mne-connectivity

mne-connectivity: A module for connectivity data analysis with MNE.

  • Documentation: https://mne-connectivity.readthedocs.io/
  • License: BSD 3-Clause License Copyright (c) 2021, MNE tools for MEG and EEG data analysis All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  • Latest release: 0.7.0
    published over 1 year ago
  • Versions: 7
  • Dependent Packages: 6
  • Dependent Repositories: 3
  • Downloads: 18,443 Last month
Rankings
Dependent packages count: 1.9%
Downloads: 4.1%
Average: 5.0%
Dependent repos count: 9.0%
Maintainers (2)
Eric89GXL adam2392
Last synced: 6 months ago
conda-forge.org: mne-connectivity

MNE-Connectivity is an open-source Python package for connectivity and related measures of MEG, EEG, or iEEG data built on top of the MNE-Python API. It includes modules for data input/output, visualization, common connectivity analysis, and post-hoc statistics and processing.

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 1
Rankings
Dependent repos count: 24.4%
Forks count: 34.8%
Average: 38.6%
Stargazers count: 43.8%
Dependent packages count: 51.6%
Last synced: 6 months ago

Dependencies

environment.yml conda
  • decorator
  • h5io
  • h5netcdf
  • joblib
  • matplotlib
  • mne
  • numpy
  • pandas
  • pillow
  • pip
  • pooch >=1.5
  • pyqt !=5.15.3
  • python >=3.8
  • pyvista >=0.32
  • pyvistaqt >=0.4
  • scipy
  • statsmodels
  • tqdm
  • vtk >=9.0.1
  • xarray
requirements.txt pypi
  • h5netcdf *
  • matplotlib *
  • mne >=1.0
  • netCDF4 *
  • numpy *
  • pandas *
  • pyqt5 >=5.10,<5.14
  • pyqt5 >=5.10,
  • pyqt5-sip *
  • pyvista >=0.30
  • pyvistaqt >=0.4
  • scipy *
  • sip *
  • tqdm *
  • xarray *
requirements_doc.txt pypi
  • memory_profiler *
  • nibabel *
  • nilearn *
  • numpydoc *
  • pooch *
  • pydata-sphinx-theme *
  • sphinx *
  • sphinx-autodoc-typehints *
  • sphinx-copybutton *
  • sphinx-gallery *
  • sphinx_rtd_theme *
  • sphinxcontrib-bibtex *
  • typing-extensions *
requirements_testing.txt pypi
  • check-manifest *
  • codespell *
  • flake8 *
  • numpydoc *
  • pydocstyle *
  • pytest *
  • pytest-cov *
  • pytest-timeout *
  • scikit-learn *
  • statsmodels *
  • twine *
  • wheel *
.github/workflows/circle_artifacts.yml actions
  • larsoner/circleci-artifacts-redirector-action master composite
.github/workflows/linux_conda.yml actions
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite
.github/workflows/unit_tests.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
  • codecov/codecov-action v1 composite