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lameg's Introduction

laMEG

Toolbox for laminar inference with MEG, powered by FreeSurfer and SPM

PyPI version Unit tests codecov linting: pylint Python 3.7 License: GPL v3 Repo Size PyPI - Downloads

Operating system

  • Windows: not supported by FreeSurfer
  • Mac: may work, but not tested
  • Linux: yes

Requirements

  • FreeSurfer v6.0, setup and configured (FREESURFER_HOME set, SetUpFreeSurfer.sh sourced, and SUBJECTS_DIR set)
  • Python version 3.7
  • Anaconda (or miniconda)

Installation

  1. 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)

  2. Activate the environment:

    conda activate <env name>
    

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

  3. To install laMEG, run:

    pip install lameg
    
  4. Before using, deactivate and reactivate the environment for changes to environment variables to take effect:

    conda deactivate
    conda activate <env name>
    
  5. If you want to run the tutorials, download and extract the test data

Documentation and Tutorials

Once you have installed laMEG, check out the example notebooks, tutorials, and documentation.

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

lameg's People

Contributors

jbonaiuto avatar danclab avatar maciekszul avatar

Stargazers

Ludovic DARMET avatar Nicholas Tolley avatar  avatar Daniel Borek avatar

Watchers

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lameg's Issues

Tutorials should use temp directory

Tutorials currently copy code from test_data to a hard-coded directory based on our server filesystem. They should create a temp directory which is removed at the end of the tutorial

Some surfaces contain unconnected vertices

Some surfaces contain unconnected vertices, likely a result of removing non-manifold edges. This affects smoothing (lameg/matlab/spm_eeg_smoothmesh_multilayer_mm.m). Maybe these vertices should be removed

Fiducial labels

Currently the fiducial labels in coregister are fixed as nas, lpa, rpa, but to work with data from Elekta scanners, they should be able to be customized (i.e. Nasion, LPA, RPA)

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