Re-awakening the Brain for Disorders of Consciousness (DoC)

Matlab implementation of the Leading Eigenvector Dynamics Analysis (LEiDA) framework and Whole-brain Hopf model

This repository contains the source code used in the study:

Dagnino, P. C., Escrichs, A., López-González, A., Gosseries, O., Annen, J., Sanz Perl, Y., Kringelbach, M. L., Laureys, S., & Deco, G. (2024). Re-awakening the brain: Forcing transitions in disorders of consciousness by external in silico perturbation. PLoS Computational Biology, 20(5), e1011350. https://doi.org/10.1371/journal.pcbi.1011350

This study explores the probabilistic metastable substates (PMS) of different diagnostic caterogories of DoC (model-free) and how in silico perturbation of whole-brain Hopf models can drive transitions in patients with DoC (model-based).

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Purpose & Scope

• Model transitions between low- and high-consciousness brain states via in silico perturbations.
• Simulate whole-brain activity derived from empirical fMRI and structural connectomes.
• Assess perturbation outcomes across diagnostic categories (e.g., UWS, MCS).
• Investigate the regional sensitivity to perturbation.

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Repository Structure

• hopf_simulations/: MATLAB scripts for simulating perturbation protocols.
• leida/: MATLAB scripts for calculating the PMS.

Note: Original patient data are not included due to privacy. Use placeholder or simulated data to test scripts.

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Requirements

• MATLAB R2018a or later
• resting-state fMRI and dMRI connectome matrices (preprocessed and in time series format)

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Usage Instructions

1. Clone the repository and add paths to MATLAB.

2. Load the empirical connectome and fMRI baseline state.

3. Run the LEiDA scripts.

4. Run the whole-brain model scripts

5. Analyze state transitions and the regions most sensitive to perturbation.

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Data Sources

• This work uses clinical neuroimaging data from patients with DoC.
• All patient data were anonymized and handled in accordance with institutional ethics guidelines.

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Citation

If you use this code, please cite:

Dagnino, P. C., Escrichs, A., López-González, A., Gosseries, O., Annen, J., Sanz Perl, Y., Kringelbach, M. L., Laureys, S., & Deco, G. (2024). Re-awakening the brain: Forcing transitions in disorders of consciousness by external in silico perturbation. PLoS Computational Biology, 20(5): e1011350. https://doi.org/10.1371/journal.pcbi.1011350

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License

This project is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

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Contact

For support or scientific questions, please contact the first author:

Paula Clara Dagnino
[email protected]
CNS Department, University Pompeu Fabra