Software and data for "In-silico molecular enrichment and clearance of the human intracranial space"

This repository provides the software and data for the paper 

Causemann, M., Kuchta, M., Masri, R., & Rognes, M. E. (2025). In-silico molecular enrichment and clearance of the human intracranial space.

In particular, it contains the following data:

file
description

code.zip

The code used to run all simulations and postprocessing steps. Also available at:

https://github.com/MariusCausemann/brain-PVS-SAS-transport

surfaces.zip

The surface triangulations extracted from the segmentations in .ply format, suitable for viewing in e.g. paraview or further processing.

standardmesh.zip

The mesh used to run all simulations in .xdmf format.

standard.xdmf : complete mesh, including markers for parenchyma and CSF spaces.

standard_outer.xdmf : only CSF spaces.

*_facets.xdmf: respective boundary markers

pvsnetworks.zip

1D representation of the arterial and venous networks, as well as the 3D cylinder corresponding to the vessel diameter. 

segmentation.zip

Synthseg segmentations of the T1 data and binary masks of venous and arterial networks from Hodneland et al.

modelA.zip

Simulation results (concentration values in CSF, parenchyma and PVS in 10min steps) for the baseline model in the paper.

modelA.html

Interactive visualization of the tracer spreading for the baseline model in the paper. Also available here.

modelA.mp4

Animation of the tracer spreading for the baseline model in the paper.

modelA-strongVM.zip

Simulation results (concentration values in CSF, parenchyma and PVS in 10min steps) for the high PVS flow model in the paper.

modelA-strongVM.html

Interactive visualization of the tracer spreading for the high PVS flow model in the paper. Also available here.

modelA-strongVM.mp4

Animation of the tracer spreading for the high PVS flow model in the paper.