System requirements:
This software was made and tested on a desktop computer (Mac OS) running Matlab 2019+

Installation guide:
Just go the main folder in Matlab and run the tda_msc_rsfmri_runmapper.m file to run Mapper on the data and tda_msc_rsfmri_anamapper.m to generate results in the manuscript

Demo:
Within tda_msc_rsfmri_anamapper.m file, each cell can be independently run to generate individual figures

Instruction for use:
You can individually run each cell in the Matlab file tda_msc_rsfmri_anamapper.m

The data can be downloaded from individual data websites as mentioned in the paper. 


License:
The work is covered under the BSD 3-Clause Clear License
More information here - https://choosealicense.com/licenses/bsd-3-clause-clear/

Cite:
Please cite the following papers if you use this code:
1. Saggar, M., Shine, J. M., Liegeois, Dosenbach, N.U.F., Fair, D. (under-review) Precision dynamical mapping using topological data analysis reveals a unique (hub-like) transition state at rest in highly sampled individuals. Nature Communications
Preprint: https://www.biorxiv.org/content/10.1101/2021.08.05.455149v2 
2. Geniesse, C., Sporns, O., Petri, G., Saggar, M. (2019). Generating dynamical neuroimaging spatiotemporal representations (DyNeuSR) using topological data analysis. Network Neuroscience. http://dx.doi.org/10.1162/netn_a_00093 
3. Saggar, M., Sporns, O., Gonzalez-Castillo, J., Bandettini, P.A., Carlsson, G., Glover, G., Reiss, A.L. (2018) Towards a new approach to visualize and quantify brain's dynamical organization using topological data analysis. Nature Communications. http://dx.doi.org/10.1038/s41467-018-03664-4
4. Saggar, Manish. "Systems and Methods for Mapping Neuronal Circuitry and Clinical Applications Thereof." U.S. Patent Application 16/171,255, filed April 25, 2019