Background

TVB is a platform for simulating whole-brain dynamics that starts from raw data involving:

  1. structural connectivity derived from DTI
  2. brain parcellation derived from MRI and CT
  3. SEEG xyz locations derived from MRI and CT

This will then determine a gain matrix to determine SEEG signals from the source signals that are generated from neural mass models. The neural mass models will be implemented with nonlinear, complex models for simulating certain type of electrophysiology. The Epileptor is used for simulating seizure activity from a specific source region.

The epileptor is a set of coupled differential equations that rely on 6 different variables. They are described here:

Data & Metadata

Generally, refer to my post on Freesurfer to establish the preprocessing data pipeline using Freesurfer, FSL and MRtrix3.

The minimum necessary requirements for creating the TVB dataset are a set of T1 and DWI images as a list of dicom files, or a single 4-D image nifti file.

A high level summary of how the pipeline proceeds is: 1. Construct Cortical Surface, Subcortical Surface

Using freesurfer, you can get the reconstructed surfaces, which are your files that outline the voxels that belong to each region of the brain. This will give you the surface geometries of the cortical and subcortical surface.

  1. Construct Parcellation Scheme

This can range from the default in freesurfer to different atlases available for the human brain. This will give you a region mapping for every vertex/face from your cortical/subcortical surface geometries files.

  1. Construct Corticography Tracts

First, you need to coregister the DWI images with the T1 scans Using the DWI images, along with the reconstructed surfaces, you can count fiber tracts between each region of the brain and reconstruct the structural connectivity matrices. This is composed from the weights matrix and the length matrix between parcellated regions.

  1. Obtain Electrode Coordinates in T1 Space

First, you need to coregister the CT reconstructed freesurfer file into the T1 space.

  1. Computing Gain Matrix Between Brain Regions and Electrodes

In order to compute forward solutions of electrode (i.e. SEEG, ECoG, etc.) activity, you need to compute a gain matrix that transforms region activity into electrode activity. This can be done using an inverse-square method fall-off on the region activity, or using a dipole method as outlined in the "Virtual Epileptic Patient" paper. Note that these methods have some limitations, as it assumes all activity from brain regions are "projected" to the iEEG electrodes instantaneously.

Implementation

1. Setting Up Environment

First you may want to set up a conda environment, or a virtualenv that will separate the entire python project from your normal OS.

pip install nibabel networkx
git clone https://github.com/the-virtual-brain/tvb-data
git clone https://github.com/the-virtual-brain/tvb-library

If you want to have a script to add these all to path for your jupyter notebook, use the following:

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#!/bin/bash
echo "Launching IPython Notebook from TVB Distribution"
if [ -z "$LANG" ]; then
    export LANG=en_US.UTF-8
fi
export LC_ALL=$LANG
# add tvb data and library to path and launch notebook
export PYTHONPATH=$(pwd)/_tvbdata:$(pwd)/_tvblibrary:$PYTHONPATH;
jupyter notebook

1b. Setting Up Environment on a Cluster

. /soft/miniconda3/activate
conda env list
conda create -n tridesclous python=3.6 scipy numpy pandas scikit-learn matplotlib seaborn pyqt=5 ipykernel
source activate tridesclous
pip install pyqtgraph
pip install https://github.com/tridesclous/tridesclous/archive/master.zip
python -m ipykernel install --name tridesclous-testing —user

2. Simulating Epilepsy

In order to simulate epilepsy, you are going to walk through a pipeline using TVB. Details are left out for now.

i. Structural Connectivity

What is the matrix of connectivities between your brain regions? Ex: Connectivity weights, conduction speed, coupling function between long-range regions

ii. Neural Mass Model

What is the phenomenological model at brain regions? Ex: Epileptor6D, with parameter settings

iii. Integrators

How to solve your stochastic differential equation? Ex: Heunstochastic, with noise levels

iv. Coupling

How are your brain regions coupled? How does activity of one region translate to the next? Is it transformed via a function? Ex: linear, additive, hyperbolic

v. Monitors

What variables to monitor and store? Ex: State variables, iEEG activity from sampling rate and period.

Then once these are complete, you can run your simulation.

References:

  1. https://github.com/the-virtual-brain/tvb-library
  2. https://github.com/the-virtual-brain/tvb-epilepsy
  3. https://www.thevirtualbrain.org/tvb/zwei