Connectivity Analysis Example Scripts

Overview

This is a set of example scripts that use the exp-info library to analyze connectivity and information transfer between channels in neural recordings.

These are not well-polished tutorial scripts. These are derived from Chris's testing and pilot analysis code. They should still be useful as a starting point for new analysis scripts.

Libraries

The scripts need libraries from the following ACC Lab GitHub repositories:

• ConditionalEntropy (low-level information calculations): https://github.com/att-circ-contrl/ConditionalEntropy
• exp-info (high-level information calculations) https://github.com/att-circ-contrl/exp-info
• exp-preproc (pre-processing and iteration routines) https://github.com/att-circ-contrl/exp-preproc
• exp-utils (miscellaneous support functions): https://github.com/att-circ-contrl/exp-utils
• LoopUtil (miscellaneous support functions): https://github.com/att-circ-contrl/LoopUtil

The following external libraries are also needed:

• The Field Trip toolbox: https://github.com/fieldtrip/fieldtrip
• The Open Ephys "analysis tools" library (for reading data saved in Open Ephys's format): https://github.com/open-ephys/analysis-tools
• The npy-matlab library (needed by Open Ephys's library; it comes with it).

Folders

• datasets -- Abbreviated datasets read by the example scripts.
• example-1-synth -- Analysis script examining a synthetic dataset with known communication patterns (generated using the SynthRobinson repository). This looks for "routing states" (pairs of channels with directional information flow).
• libraries -- Symbolic links to the various libraries used by the scripts. These will only work on my system; modify them or add library paths to Matlab manually to run the scripts on your own system.

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