adam2392 / interictal_study

EZTRACK Interictal Study

Master repo with eztrack's UI, data manager, and analysis backend.

Data Organization

Data should be organized in the BIDS-iEEG format:

https://github.com/bids-standard/bids-specification/blob/master/src/04-modality-specific-files/04-intracranial-electroencephalography.md

Additional data components:

1. electrode_layout.xlsx
    A layout of electrodes by contact number denoting white matter (WM), outside brain (OUT), csf (CSF), ventricle (ventricle), or other bad contacts.

2. clinical_metadata.xlsx
    A database column layout of subject identifiers and their metadata.

Installation Guide

Setup environment from pipenv

pipenv install --dev

# use pipenv to install private repo
pipenv install -e [e-mail]:adam2392/eztrack

# or
pipenv install -e /Users/adam2392/Documents/eztrack
pipenv install -e /home/adam2392/Documents/eztrack


# if dev versions are needed
pipenv install https://api.github.com/repos/mne-tools/mne-bids/zipball/master

To install the MTMORF version of [rerf](https://sporf.neurodata.io/install.html):

# git clone SPORF package

# make sure you are on the mtmorf branch cd packedForest make

# pip install local cd ../Python pip install -e .

Setup Jupyter Kernel To Test

You need to install ipykernel to expose your environment to jupyter notebooks.

python -m ipykernel install --name iistudy --user
# now you can run jupyter lab and select a kernel
jupyter lab