  We present BrainPainter, a software that automatically generates images of
highlighted brain structures given a list of numbers corresponding to the
output colours of each region. Compared to existing visualisation software
(i.e. Freesurfer, SPM, 3D Slicer), BrainPainter has three key advantages: (1)
it does not require the input data to be in a specialised format, allowing
BrainPainter to be used in combination with any neuroimaging analysis tools,
(2) it can visualise both cortical and subcortical structures and (3) it can be
used to generate movies showing dynamic processes, e.g. propagation of
pathology on the brain. We highlight three use cases where BrainPainter was
used in existing neuroimaging studies: (1) visualisation of the degree of
atrophy through interpolation along a user-defined gradient of colours, (2)
visualisation of the progression of pathology in Alzheimer's disease as well as
(3) visualisation of pathology in subcortical regions in Huntington's disease.
Moreover, through the design of BrainPainter we demonstrate the possibility of
using a powerful 3D computer graphics engine such as Blender to generate brain
visualisations for the neuroscience community. Blender's capabilities, e.g.
particle simulations, motion graphics, UV unwrapping, raster graphics editing,
raytracing and illumination effects, open a wealth of possibilities for brain
visualisation not available in current neuroimaging software. BrainPainter is
customisable, easy to use, and can run straight from the web browser:
https://brainpainter.csail.mit.edu , as well as from source-code packaged in a
docker container: https://github.com/mrazvan22/brain-coloring . It can be used
to visualise biomarker data from any brain imaging modality, or simply to
highlight a particular brain structure for e.g. anatomy courses.
