BrainVis: A cloud-connected 3D exploration and visualization tool for multi-modal
Vesna Prčkovska , Tim Peeters , David Moreno-Dominguez , and Paulo Rodrigues
Mint Labs, Barcelona, Spain
Diusion MRI tractography is central to the study of complex brain circuitry since it is the only non-invasive technique capable of measuring the brain’s
wiring. Data visualization gets increasingly complex as tractography is combined with morphometric results in structural connectomes, and even more so
when coupled with functional information from fMRI techniques. Such complex imagery, aggregating multi-modal information, 3D meshes, and statistical
maps is often visualized using research tools with complicated user interfaces (UIs) and cluttered visualizations.
BrainVis is a sophisticated, free 3D neuroimaging visualization tool with a simple UI aimed for eective exploration of neuroimaging data towards
demonstrating neurobiological ndings.
Data visualization is an important aspect of neuroimaging: paramount for correct and intuitive interpretation of results and key for neurosurgical
planning. However, there is a lack of standardization in the current viewers, with various le types and data structures. Many viewers lack truly interactive
3D view and consistent or specialized development support.
We developed BrainVis to alleviate these problems: it is a fully interactive 3D viewer, where multiple modalities can be shown simultaneously. Advanced
tools are provided such as surface rendering and interactive exploration of tractography streamlines. Seamless integration with a cloud-system provides
transparent fetching and processing of data. For user interface (UI) simplicity, it features adaptive menus that only show the options applicable to the
current data. It can be coupled with Leap Motion hardware for intuitive touchless interaction.
Various tools exist for computing dierent aspects of neuroimaging data, from structural morphometric maps (brain tissue segmentation, cortical
volumes, cortical thickness), to structural connectivity (e.g., dMRI tractography), and structural connectomes or resting state functional connectomes. In
parallel, we developed a cloud-based platform providing a standardized place for neuroimaging data management and image processing pipelines. All
computations can be run in the cloud environment, and the generated result les are kept in a managed data warehouse. All les (input and output) can
be retrieved through an application programming interface (API).
Desktop Application Implementation
BrainVis is a freely available desktop application developed to display the processed data in 3D for Windows, Linux and MacOS. With an active Internet
connection, BrainVis can search and download the processed neuroimaging studies (e.g., brain tissue segmentation, tractography, structural
connectomes) and visualize the respective data. Data les can also be downloaded from the cloud platform through the web browser. The cross-platform
Features and User Interface
BrainVis is seamlessly integrated with the cloud infrastructure. The user simply selects which analysis to download and visualize, and all necessary les
are automatically retrieved without manual selection of the dierent les and parameters. BrainVis has three main components:
1. Adaptive options menu: The available options are automatically enabled if the corresponding data is available. For example, the 3D region-of-interest
(ROI) selection for tractography is only visible if tractography maps are loaded. This way a simple and sleek UI is ensured.
2. Interactive 3D view: The application is focused on maximizing the 3D view and exploration. It allows multi-modal visualization of structural data, as well
as overlays of segmentation analysis, lesion masks, tumor masks, FA maps, and tractography maps. It also provides 3D surface mesh generation for
cortical region visualization and advanced ber selection options.
3. 2D slices view: also interactive allowing users to click on a plane and the respective 2D position sets the 3D cursor in the view.
Multi-modal data is seamlessly enabled, the cursor position is checked against cortical label map, and the corresponding brain region is highlighted and
thus can be used to select ber-tracts.
There are several options for Interactive Fiber Selection: 2D plane ber selection; Spherical ROI with AND/OR ltering options (Figure 1a); Highlighting
bundles in ROI (Figure 1b); Filtering by cortical regions (Figure 1c). Exporting ber selections to external tools and applications (e.g., export to .stl format
for 3D printing as in Figure 2).
All these capabilities make BrainVis a exible tool suited for multiple scenarios. Several use-case examples follow: Figure 3 illustrates the visualization of
morphometric analysis pipeline applied to a healthy subject; Figure 4 shows a tumor case where the bers are automatically generated by seeding from
an fMRI motor task and in Figure 5 the lesions of a patient with multiple sclerosis have been projected onto tractography streamlines helping elucidate
what connections might be more severely aected by the disease.
In order to provide a better solution for the physicians and specically neurosurgeons for the data visualization, we oer a fully touchless interface
(Figure 1d). We use Leap Motion tracking device that detects and tracks hands, ngers, and nger-like tools. This touchless interface provides an intuitive
and natural way to explore 3D brain maps, especially towards precise moving of the ROI in 3D space, and has a direct application potential in
1 1 1 1
BrainVis oers a well-rounded option for various neuroimaging visualization needs. It oers convenient access to the detailed 3D-neuroimaging data and
the ability to perform data-mining and visualization of neuroanatomy in an integrated manner. This should greatly increase the power and benet of
neuroimaging informatics for the researchers in this eld.
No acknowledgement found.
Figure 1: Dierent ber selection modes: a) ber selection by ROI located in the left caudal middle frontal region b) white matter bundles highlighted as
bers cross the selected ROIs c) ltering the selected cortical regions: precentral, postcentral and brainstem d) interactive ROI placement within the 3D
space of the ber tracts of the brain in a touchless manner simply by moving the ngers.
Figure 2: 3D print case exported from BrainVis. The tumor is in the frontal lobe surrounded by the pushed white matter tracts. The right hemisphere is
printed as a hollow surface from the segmented cortical mesh.
Figure 3: The cortical brain structures can be seen overlayed over the skull-stripped structural T1 image. We can also observe the 3D surface generated
for precentral and postcentral regions. The spatial position highlights the precuneus region and its coordinates (see box with text down right).