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brain_eigenmodes

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# Eigenmodes of the Brain: Revisiting Connectomics and Geometry

![banner image](https://github.com/sina-mansour/brain_eigenmodes/blob/main/readme.png?raw=true)

This repository contains code and data supporting our recent manuscript titled "Eigenmodes of the Brain: Revisiting Connectomics and Geometry." Our study explores specific aspects discussed in the article ["Geometric Constraints on Human Brain Function" (Pang et al. 2023)](https://doi.org/10.1038/s41586-023-06098-1).

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## Repository Contents

The repository includes Jupyter notebooks (located in the `notebooks` directory) that comprehensively describe the analytical procedures necessary to reproduce the results discussed in our manuscript. Additionally, several scripts (located in the `scripts` directory) utilized in our analyses are provided. Supplementary data required to replicate our findings is also included.

### Reproducible Notebooks

The `notebooks` directory contains three notebooks that collectively detail the steps to reproduce our results:

1. **Notebook 1: Alternative Brain Eigenmodes**: Scripts generating all brain eigenmodes utilized in this study.
2. **Notebook 2: Reconstruction Accuracy**: Scripts computing reconstruction accuracy from HCP's rest and task data.
3. **Notebook 3: Reproducible Results**: Scripts generating all figures presented in our manuscript.

### Accompanying Scripts

#### Automated Systematic Evaluations

We conducted a systematic analysis in our supplementary evaluations to assess the influence of various connectome mapping parameters and decisions on reconstruction accuracy. Bash and Python scripts for these evaluations (executed on a high-performance computing cluster) are available in the `scripts` directory.

#### Procrustes Analysis

As part of our supplementary evaluations, we conducted a Procrustes analysis using several Matlab scripts provided in the `scripts` directory.

### Provided Data

We've included minimal data within this repository to facilitate reproducibility of our findings:

- Our group average connectome (from the new tractography pipeline, without any smoothing) is available in the `data/connectomes` directory.
- Eigenmodes from our connectome reconstruction pipeline (using weighted, smoothed connectivity) are provided in the `data/eigenmodes` directory for easy access without the need to execute the scripts in Notebook 1.
- Additionally, several template files used in our analyses are included in the `data/templates` directory.

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## Get in Touch

If you're considering using the provided data for your own research purposes beyond reproducing our findings, we're here to help! Feel free to contact us at:

[![sina \[dot\] mansour \[dot\] lakouraj \[at\] gmail](https://img.shields.io/badge/Contact-sina%20[dot]%20mansour%20[dot]%20lakouraj%20[at]%20gmail-blue)](https://sina-mansour.github.io/)

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