aspire-alphacsc-epilepsy-MEG

Plots and analysis for the paper "Data-driven approach for the delineation of the irritative zone in epilepsy in MEG"

Quick start

Create a new Anaconda environment:

conda create -n megspikes-pipeline python=3.7
conda activate megspikes-pipeline

The easiest way to install the megspikes package is using pip. You should clone the repository and install all dependencies:

git clone --depth 1 --branch v0.1.4 https://github.com/MEG-SPIKES/megspikes.git
cd megspikes/
pip install .

To install the correct kernel for Jupyter Notebook use the following command:

python -m ipykernel install --user --name megspikes-pipeline

Additionally, to plot paper images Seaborn package is needed.

pip install seaborn

All the pipelines are in the analysis folder. Additionally, case_info.yml file in the analysis folder is required. The structure of the case_info.yml file:

case_name:
  1: SAMPLE1
  2: SAMPLE2
cases_path: /aspire-alphacsc/Cases
free_surfer_path: /aspire-alphacsc/FreeSurfer