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.

Understanding how higher order cognitive function emerges from the underlying brain structure depends on quantifying how the behaviour of discrete regions are integrated within the broader cortical landscape. Recent work has established that this macroscale brain organization and function can be quantified in a compact manner through the use of 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. More generally, its macroscale perspective on brain organization offers novel possibilities to investigate the complex relationships between brain structure, function, and cognition in a quantified manner. Here, we present a compact workflow and open-access toolbox that allows for (i) the identification of gradients (from structural or functional imaging data), (ii) their alignment (across subjects or modalities), and (iii) their visualization (in embedding or cortical space). Our toolbox also allows for controlled association studies between gradients with other brain-level features, adjusted with respect to several null models that account for spatial autocorrelation. The toolbox is implemented in both Python and Matlab, programming languages widely used by the neuroimaging and network neuroscience communities. Several use-case examples and validation experiments demonstrate the usage and consistency of our tools * Corresponding author Email address: boris.bernhardt@mcgill.ca (Boris C. Bernhardt) 1 Authors contributed equally to this work.

The adult functional connectome is well characterized by a macroscale spatial gradient of connectivity traversing from unimodal toward higher-order transmodal cortices that recapitulates known principles of hierarchical organization and myelination patterns. Despite an emerging literature assessing connectome properties in neonates, the presence of connectome gradients and particularly their correspondence to microstructure remains largely unknown. We derived connectome gradients using unsupervised techniques applied to functional connectivity data from 40 term-born neonates. A series of cortex-wide analysis examined associations to magnetic resonance imaging-derived morphological parameters (cortical thickness, sulcal depth, curvature), measures of tissue microstructure (intracortical T1w/T2w intensity, superficial white matter diffusion parameters), and subcortico-cortical functional connectivity. Our findings indicate that the primary neonatal connectome gradient runs between sensorimotor and visual anchors and captures specific associations to cortical and superficial white matter microstructure as well as thalamo-cortical connectivity. A second gradient indicated an anterior-to-posterior asymmetry in macroscale connectivity alongside an immature differentiation between unimodal and transmodal areas, indicating a connectome-level circuitry en route to an adult-like organization. Our findings reveal an important coordination of structural and functional interactions in the neonatal connectome across spatial scales. Observed associations were replicable across individual neonates, suggesting consistency and generalizability.