BrainPainter: A Software for the Visualisation of Brain Structures, Biomarkers and Associated Pathological Processes
Name
1905.08627.pdf
Description
Submitted version
Size
5.37 MB
Format
Adobe PDF
Checksum (MD5)
67327d55971bc6935861a71494486322
Author(s)
Marinescu, Razvan V
Eshaghi, Arman
Alexander, Daniel C.
Golland, Polina
Date Issued
October 2019
Journal
Lecture Notes in Computer Science
Publisher
Springer International Publishing
Citation
Marinescu, Răzvan V. et al. "BrainPainter: A Software for the Visualisation of Brain Structures, Biomarkers and Associated Pathological Processes." MBIA 2019, MFCA 2019: Multimodal Brain Image Analysis and Mathematical Foundations of Computational Anatomy, Lecture Notes in Computer Science, 11846, Springer International Publishing, 2019, 112-120. © 2019 Springer Nature Switzerland
Version
Original manuscript
Abstract
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 (Source code: https://github.com/mrazvan22/brain-coloring ) is customisable, easy to use, and can run straight from the web browser: http://brainpainter.csail.mit.edu. 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.
Description
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11846)
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Terms of Use
Creative Commons Attribution-Noncommercial-Share Alike
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1007/978-3-030-33226-6_13
