BrainSpace: a toolbox for the analysis of macroscale gradients in neuroimaging and connectomics datasets.

Communications Biology
Reinder Vos de WaelBoris Bernhardt

Abstract

Understanding how cognitive functions emerge from brain structure depends on quantifying how discrete regions are integrated within the broader cortical landscape. Recent work established that macroscale brain organization and function can be described in a compact manner with multivariate machine learning approaches that identify manifolds often described as cortical gradients. By quantifying topographic principles of macroscale organization, cortical gradients lend an analytical framework to study structural and functional brain organization across species, throughout development and aging, and its perturbations in disease. Here, we present BrainSpace, a Python/Matlab toolbox for (i) the identification of gradients, (ii) their alignment, and (iii) their visualization. Our toolbox furthermore allows for controlled association studies between gradients with other brain-level features, adjusted with respect to null models that account for spatial autocorrelation. Validation experiments demonstrate the usage and consistency of our tools for the analysis of functional and microstructural gradients across different spatial scales.

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Citations

May 20, 2020·Communications Biology·Yifei WengBoris C Bernhardt
Sep 4, 2020·NeuroImage·Patrick FriedrichMichel Thiebaut de Schotten
Jun 26, 2020·NeuroImage·Joshua B BurtJohn D Murray
Jan 18, 2021·NeuroImage·Xinyu LiangGaolang Gong
Feb 21, 2021·Communications Biology
Apr 16, 2021·NeuroImage·Ross D Markello, Bratislav Misic
May 6, 2021·Cell Reports·Zirui HuangAnthony G Hudetz
Aug 24, 2020·NeuroImage·Richard A I BethlehemKamen A Tsvetanov
Jun 16, 2021·Communications Biology·Bo-Yong ParkBoris C Bernhardt
Jul 1, 2021·Network Neuroscience·Giulia LioiNicolas Farrugia
Feb 4, 2021·Annual Review of Neuroscience·Rogier B MarsMatthew F S Rushworth
Jul 23, 2021·Science Advances·Ryan V RautMarcus E Raichle
Mar 18, 2021·Brain : a Journal of Neurology·Qiongling LiBoris C Bernhardt
Sep 17, 2021·Communications Biology·Oualid BenkarimBoris C Bernhardt

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Methods Mentioned

BETA
PCA

Software Mentioned

BrainSpace
Python
FreeSurfer
Matlab
Procrustes
CIVET
Mesulam
BrainSpace toolbox

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