Connectome
This tool allows to visualize the Connectome that describes how the regions of the brain are interconnected. Particularly, the tools enable the user to explore the intrinsic geometry of the brain connectome, by letting he/she switch quickly between different topological spaces where the connectome is embedded. The mathematical foundations of BRAINtrinsic are described in [3]. With a simple and easy-to-use interface, users can explore all the connections with a edge-on-demand technique and focus on very specific area by switching on and off regions of the brain. Simple analytics such as nodal strength and shortest path trees can be computed on the fly. This tool has been developed with virtual reality in mind and it is compatible with Head Mounted Displays such as Oculus Rift (both DK1 and DK2).
How to use it
This tool has been optimized for Google Chrome Browser. Users can upload data and visualize them. All the files needed are in ".csv" format and specifically should be structured as follows:
- Centroid files (4): each of them contains different ROI coordinates (the "centroid"). Each row of the file contains three values that represent the x,y,z coordinates. Each value is separated by a comma.
- network file: this file contains the adjacency matrix of the connectome network. Each value within the same row is separated by a comma. The tool is optimized to deal with weighted graph.
- labelkey file: each row contains the Freesurfer ID label to which the node belongs.
Desktop Demo
The desktop version of BRAINtrinsic is available here.
Virtual Reality
BRAINtrinsic is fully compatible with Head Mounted Displays such as Oculus Rift (both DK1 and DK2). Before starting the tool, download the plug-in "oculus-rest", available here for Mac OS users (more information here). Check out our OR-compatible demo here (DK1) or here (DK2). If you want to upload you own data, go to the upload page and select the version of Oculus Rift you are using.
Matlab code
The Matlab toolbox can be downloaded here.
Color Coding
BRAINtrinsic allows three different color coding schemas:
- Anatomy - nodes are grouped according to their neuroanatomical locations.
- Embeddedness - nodes that have been shown to be highly embedded in the human structural connectome [1] are highlighted.
- Rich-club - Rich-club nodes as defined in [2] are highlighted. Note that the Rich-club regions form a subset of highly-embedded nodes.
Acknowledgement
BRAINtrinsic is the result of collaboration between computer scientists and psychiatrists. Giorgio Conte, who wrote the code of the tool, and Dr. Angus Forbes belong to Creative Coding Research Group which is part of Electronic Visualization Lab (EVL) at University of Illinois of Chicago (UIC). Dr. Alex Leow, Dr. Olusola Ajilore, and Dr. Allen Ye belong to UIC Department of Psychiatry. BRAINtrinsic is an integral research component of the CoNECt@UIC, an interdisciplinary team of researchers and clinicians devoted to improving the understanding of brain connectivity.
References
[1] - Ye, A. Q., Zhan, L., Conrin, S., GadElKarim, J., Zhang, A., Yang, S., ... & Leow, A. (2015). Measuring embeddedness: Hierarchical scale‐dependent information exchange efficiency of the human brain connectome. Human Brain Mapping.
[2] - van den Heuvel, M. P., & Sporns, O. (2011). Rich-club organization of the human connectome. The Journal of neuroscience, 31(44), 15775-15786.
[3] - Conte, G., Ye, A. Q., Forbes, A. G., Ajilore, O., & Leow, A. (2015). BRAINtrinsic: A Virtual Reality-Compatible Tool for Exploring Intrinsic Topologies of the Human Brain Connectome. Accepted to appear in the proceedings of
Brain Informatics and Health, 30 August - 2 September 2015, London, UK.