Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

A hands-on tutorial on network and topological neuroscience

Eduarda Gervini Zampieri Centeno, Giulia Moreni, Chris Vriend, Linda Douw, Fernando Antônio Nóbrega Santos
doi: https://doi.org/10.1101/2021.02.15.431255
Eduarda Gervini Zampieri Centeno
1Amsterdam UMC, Vrije Universiteit Amsterdam, Anatomy and Neurosciences, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, Netherlands
2Bordeaux Neurocampus, Université de Bordeaux, Institut des Maladies Neurodégénératives, CNRS UMR 5293, 146 Rue Léo Saignat, Bordeaux, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Giulia Moreni
1Amsterdam UMC, Vrije Universiteit Amsterdam, Anatomy and Neurosciences, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chris Vriend
1Amsterdam UMC, Vrije Universiteit Amsterdam, Anatomy and Neurosciences, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, Netherlands
3Amsterdam UMC, Vrije Universiteit Amsterdam, Psychiatry, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Linda Douw
1Amsterdam UMC, Vrije Universiteit Amsterdam, Anatomy and Neurosciences, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Fernando Antônio Nóbrega Santos
1Amsterdam UMC, Vrije Universiteit Amsterdam, Anatomy and Neurosciences, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: f.nobregasantos@amsterdamumc.nl
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

Abstract

The brain is an extraordinarily complex system that facilitates the efficient integration of information from different regions to execute its functions. With the recent advances in technology, researchers can now collect enormous amounts of data from the brain using neuroimaging at different scales and from numerous modalities. With that comes the need for sophisticated tools for analysis. The field of network neuroscience has been trying to tackle these challenges, and graph theory has been one of its essential branches through the investigation of brain networks. Recently, topological data analysis has gained more attention as an alternative framework by providing a set of metrics that go beyond pair-wise connections and offer improved robustness against noise. In this hands-on tutorial, our goal is to provide the computational tools to explore neuroimaging data using these frameworks and to facilitate their accessibility, data visualisation, and comprehension for newcomers to the field. We will start by giving a concise (and by no means complete) overview of the field to introduce the two frameworks, and then explain how to compute both well-established and newer metrics on resting-state functional magnetic resonance imaging. We use an open-source language (Python) and provide an accompanying publicly available Jupyter Notebook that uses data from the 1000 Functional Connectomes Project. Moreover, we would like to highlight one part of our notebook that is solely dedicated to realistic visualisation of high order interactions in brain networks. This pipeline provides three-dimensional (3-D) plots of pair-wise and higher-order interactions projected in a brain atlas, a new feature tailor-made for network neuroscience.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/multinetlab-amsterdam/network_TDA_tutorial

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted February 16, 2021.
Download PDF

Supplementary Material

Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
A hands-on tutorial on network and topological neuroscience
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
A hands-on tutorial on network and topological neuroscience
Eduarda Gervini Zampieri Centeno, Giulia Moreni, Chris Vriend, Linda Douw, Fernando Antônio Nóbrega Santos
bioRxiv 2021.02.15.431255; doi: https://doi.org/10.1101/2021.02.15.431255
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
A hands-on tutorial on network and topological neuroscience
Eduarda Gervini Zampieri Centeno, Giulia Moreni, Chris Vriend, Linda Douw, Fernando Antônio Nóbrega Santos
bioRxiv 2021.02.15.431255; doi: https://doi.org/10.1101/2021.02.15.431255

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Neuroscience
Subject Areas
All Articles
  • Animal Behavior and Cognition (4858)
  • Biochemistry (10802)
  • Bioengineering (8046)
  • Bioinformatics (27314)
  • Biophysics (13987)
  • Cancer Biology (11130)
  • Cell Biology (16062)
  • Clinical Trials (138)
  • Developmental Biology (8788)
  • Ecology (13298)
  • Epidemiology (2067)
  • Evolutionary Biology (17364)
  • Genetics (11689)
  • Genomics (15926)
  • Immunology (11034)
  • Microbiology (26114)
  • Molecular Biology (10655)
  • Neuroscience (56597)
  • Paleontology (418)
  • Pathology (1733)
  • Pharmacology and Toxicology (3005)
  • Physiology (4551)
  • Plant Biology (9644)
  • Scientific Communication and Education (1615)
  • Synthetic Biology (2690)
  • Systems Biology (6979)
  • Zoology (1510)