Meg information based connectivity coding session

!Under Construction - will be finalized by Friday!

We will be meeting virtually over Zoom from 1pm-3pm with breakout rooms for questions and collaboration
There will be a quick discussion/demo (10-20mins) and some example data on biowulf.

FRITES toolbox

Club MEG Presentation Recording

 Background
 Getting Started Scripts
 Example Scripts

Install in new environment (RECOMMENDED!):

 conda create -n frites conda-forge::mne conda-forge::jupyterlab pip -y 
 conda activate frites
 pip install frites

 git clone https://github.com/brainets/CookingFrites.git
 cd CookingFrites
 jupyter lab
 #Once jupyter is open, the notebooks are in the notebooks folder

Install in current environment (Better to use New environment as listed above!)-

 #Download getting started tutorials
 git clone https://github.com/brainets/CookingFrites.git
 pip install frites

SAM Symoblic Transfer Entropy Connectivity - (tutorial will be formalized by Friday)

Background

Club MEG SAM Connectivity Presentation Recording

Recommendations

This process is a trigger-free process that estimates the symbolic transfer entropy (connectivity assessed by delayed propagation of signals) between two ROIs 70-185Hz has been tested Use an atlas based input for the bivariate connectivity assessment SAMwts or Patch_wts to create the beamformer Output is a text file Must determine an embedding dimension (4 as default) - the higher the embedding the more data needed Minimal requirements (1Khz sampling rate and 300s of data) The inputs do not need to be brain regions (for example can compare STE between audio track to brain region)

Use on Biowulf

 #Log into biowulf
 sinteractive --mem=6G --cpus-per-task=4
 #Make sure modules are loadable -- this can also be added to ~/.bashrc file
 module use --append /data/MEGmodules/modulefiles
 module load SAMsrcDEV

 #This part is already done
 sam_cov ...
 sam_wts ...
 STEdelay ....  

cp ***TESTDATA*** (fix this part) Local folder