Metadata-Version: 2.1
Name: lameg
Version: 0.0.6
Summary: A toolbox for laminar inference with MEG
Home-page: https://github.com/danclab/laMEG
Author: DANC lab
Author-email: James Bonaiuto <james.bonaiuto@isc.cnrs.fr>, DANC lab <danclab.info@gmail.com>
Project-URL: homepage, https://github.com/danclab/laMEG
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved
Classifier: Programming Language :: Python
Classifier: Topic :: Software Development
Classifier: Topic :: Scientific/Engineering
Classifier: Operating System :: Unix
Requires-Python: ~=3.7
Description-Content-Type: text/x-rst
License-File: LICENSE

|Logo|

Toolbox for laminar inference with MEG, powered by `FreeSurfer <https://surfer.nmr.mgh.harvard.edu/fswiki>`_ and `SPM <https://github.com/spm/>`_

|PyPI version| |Unit tests| |Coverage| |Linting| |Python| |License| |Repo size| |PyPI downloads|

Operating system
================
* Windows: Tested on WSL (using Ubuntu 24.04.1), follow instructions `here <https://github.com/danclab/laMEG/blob/main/windows_instructions.md>`_
* Mac: May work, not tested
* Linux: Tested on Ubuntu and Debian

Requirements
============
* `FreeSurfer v6.0 <https://surfer.nmr.mgh.harvard.edu/fswiki/rel6downloads>`_
* Python version 3.7
* Anaconda (or miniconda)
* git
* curl

Installation
============
1. Install git and curl if needed::
       
       sudo apt-get install git curl

2. Create a conda environment::

       conda create -n <env name> python=3.7

   replacing ``<env name>`` with the name of the environment you would like to create (i.e. 'lameg', or the name of your project)

3. Activate the environment::

       conda activate <env name>

   replacing ``<env name>`` with name of the environment you created.

4. Install FreeSurfer, following the instructions `on this page <https://github.com/danclab/laMEG/blob/main/freesurfer_instructions.md>`_

5. To install ``laMEG``, run::

       pip install lameg

   This also installs SPM standalone and Matlab runtime, which can take some time depending on your connection speed.

6. Before using, deactivate and reactivate the environment for changes to environment variables to take effect::

       conda deactivate
       conda activate <env name>

7. If you want to run the tutorials, download and extract the `test data <https://osf.io/mgz9q/download>`_

Documentation and Tutorials
===========================
Once you have installed ``laMEG``, check out the
`example notebooks <https://github.com/danclab/laMEG/tree/main/examples>`_,
`tutorials <https://github.com/danclab/laMEG/tree/main/tutorials>`_, and
`documentation <https://danclab.github.io/laMEG/>`_.
For guidelines on MRI sequences, head-cast construction, and co-registration, see the `wiki <https://github.com/danclab/laMEG/wiki>`_

Funding
=======
*Supported by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme grant agreement 864550, and a seed grant from the Fondation pour l'Audition.*

|ERC| |FPA|


.. |Logo| image:: https://github.com/danclab/laMEG/blob/main/lameg/assets/logo.png?raw=true
   :alt: laMEG
   :width: 300

.. |PyPI version| image:: https://badge.fury.io/py/lameg.svg
   :target: https://badge.fury.io/py/lameg
   :alt: PyPI version

.. |Unit tests| image:: https://github.com/danclab/laMEG/actions/workflows/python-package-conda.yml/badge.svg
   :target: https://github.com/danclab/laMEG/actions/workflows/python-package-conda.yml
   :alt: Unit tests

.. |Coverage| image:: https://codecov.io/gh/danclab/laMEG/branch/main/graph/badge.svg
   :target: https://codecov.io/gh/danclab/laMEG
   :alt: codecov

.. |Linting| image:: https://img.shields.io/badge/linting-pylint-yellowgreen
   :target: https://github.com/pylint-dev/pylint
   :alt: linting: pylint

.. |Python| image:: https://img.shields.io/badge/Python-3.7-blue.svg
   :target: https://www.python.org/downloads/
   :alt: Python 3.7

.. |License| image:: https://img.shields.io/badge/License-GPLv3-blue.svg
   :target: https://www.gnu.org/licenses/gpl-3.0
   :alt: License: GPL v3

.. |Repo size| image:: https://img.shields.io/github/repo-size/danclab/laMEG
   :alt: Repo Size

.. |PyPI downloads| image:: https://img.shields.io/pypi/dm/lameg
   :alt: PyPI - Downloads

.. |ERC| image:: https://github.com/danclab/laMEG/blob/main/lameg/assets/erc_logo.jpg?raw=true
   :alt: ERC
   :height: 100

.. |FPA| image:: https://github.com/danclab/laMEG/blob/main/lameg/assets/fpa_logo.png?raw=true
   :alt: FPA
   :height: 100

