HMM_pipeline

Base HMM code should be cloned from : https://github.com/OHBA-analysis/HMM-MAR

This repository contains all the upto date code for different types of HMM analysis not necessarily pertaining to a specific paper.

eLife pipeline

In order to run HMM all the neccessary code is present in the repository.

Clone a local copy of https://github.com/OHBA-analysis/HMM-MAR

Clone a local copy of this repository.

Run the script Complete_HMM_Pipeline.m

For creating the figures in the paper

Ring figures

Figure 1 can be plotted as a regular Matlab figure using the variable supply_profiles

Use the script ReLabel.m for part A and C of the figures

Use the script Across_HMMs_connection_testing.m for part B of the figures.

Temporal properties

Use the script errorbar_plot.m

For any missing code or errors please raise an issue