Create a normative vascular continuum across the cortex and contextualize to brain organization.
/results/: dfs, maps constructed in scripts
/figs/: outcome figure in main approach (overlap 0.2)
/robustness/: outcome figure in robustness approaches (overlap 0.1, 0.15, 0.25, 0.3)
Scripts:
create_distance.py -> create_continuum.py -> all main analyses in load_pattern.py, with construction of nonlinear fit and inflection point plots in R (main_fullcircular.R)
Dependencies and required files:
Python packages: numpy, pandas, seaborn (abbreviated sbn, not sns), nibabel, brainspace (Vos de Wael et al., 2020), neuromaps, (Markello et al., 2022), scipy, matplotlib, sklearn. Python 3.8 used here for best compliance with BrainSpace.
The gene df is from the ENIGMA toolbox (Lariviere et al., 2021) and abagen (Markello et al., 2021).
Some dependencies are not included in this repo due to file size constraints. These are cortical maps of the Yeo functional networks (obtainable from BrainSpace, Lariviere et al., 2023) and cortical types (ENIGMA toolbox, Lariviere et al., 2021), the gene df (see above), and first derivative dataframes that are constructed with the given scripts. In addition, surface files are outside the main repository but can be obtained from multiple sources, including BrainSpace.
Preprint: tba
Presentations: Weber CF, Valk SL at Congress of Neurological Surgeons 2025, Child Neurology Society 2025, Neonatal Stroke Conference at Utrecht Medical Center 2025, Organization for Human Brain Mapping 2026
Larivière S, Paquola C, Park BY, Royer J, Wang Y, Benkarim O, Vos de Wael R, Valk SL, Thomopoulos SI, Kirschner M, Lewis LB, Evans AC, Sisodiya SM, McDonald CR, Thompson PM, Bernhardt BC. The ENIGMA Toolbox: multiscale neural contextualization of multisite neuroimaging datasets. Nat Methods. 2021 Jul;18(7):698-700. doi: 10.1038/s41592-021-01186-4.
Larivière S, Bayrak Ş, Vos de Wael R, Benkarim O, Herholz P, Rodriguez-Cruces R, Paquola C, Hong SJ, Misic B, Evans AC, Valk SL, Bernhardt BC. BrainStat: A toolbox for brain-wide statistics and multimodal feature associations. Neuroimage. 2023 Feb 1;266:119807. doi: 10.1016/j.neuroimage.2022.119807.
Markello RD, Arnatkeviciute A, Poline JB, Fulcher BD, Fornito A, Misic B. Standardizing workflows in imaging transcriptomics with the abagen toolbox. Elife. 2021 Nov 16;10:e72129. doi: 10.7554/eLife.72129.
Markello RD, Hansen JY, Liu ZQ, Bazinet V, Shafiei G, Suárez LE, Blostein N, Seidlitz J, Baillet S, Satterthwaite TD, Chakravarty MM, Raznahan A, Misic B. neuromaps: structural and functional interpretation of brain maps. Nat Methods. 2022 Nov;19(11):1472-1479. doi: 10.1038/s41592-022-01625-w.
Vos de Wael R, Benkarim O, Paquola C, Lariviere S, Royer J, Tavakol S, Xu T, Hong SJ, Langs G, Valk S, Misic B, Milham M, Margulies D, Smallwood J, Bernhardt BC. BrainSpace: a toolbox for the analysis of macroscale gradients in neuroimaging and connectomics datasets. Commun Biol. 2020 Mar 5;3(1):103. doi: 10.1038/s42003-020-0794-7.