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Categories: Brain Brain connection Brain connectivity Cartography CMKT Connectome Mapping ToolKit Fiber connections Neuroscience Open source program

An Open Source Program For Understanding the Brain

A new technology allowing for a detailed cartography of the fiber connections made in the brain is now available as an open source program.

A joint study from EPFL and the University of Lausanne (UNIL) and the University Hospital (CHUV), in collaboration with Harvard Medical School, has produced a powerful new computer program that analyzes the diffusion of water molecules in the brain to develop a map of the brains connection. The maps created by this program allow for an in-depth comparative study of different afflictions related to brain connectivity such as epilepsy and schizophrenia. It is now available free of charge as an open source program for all hospitals and researchers in the field of neurosciences.

“By making this program Open Source, we are contributing to a scientific community where increasing numbers of scientists are freely sharing their work,” explains Jean-Philippe Thiran, an EPFL professor and head of the Signal Processing Laboratory 5. “This way the entire community can improve and build upon work done by others.”

Researchers from hospitals, research centers and universities are able to download the program from the website, and use it for their proper research in brain connectivity.

Called Connectome Mapping ToolKit (CMKT), the program allows for individualized maps of vital brain connectivity that could aide in advancing research for epilepsy, schizophrenia, and even post-trauma patient rehabilitation.

“Our program brings together a series of processes,” further explains Jean-Philippe Thiran. “It begins with an individual MRI that gives precise information about the capacity of water molecule diffusion and then deducts a map, at the macroscopic scale, of the millions of fibers in the brain. It is then possible to observe the connections between the different regions of the brain and compare them with brains from other patients.”

This novel program will considerably open the field of neurobiological research by allowing for an unprecedented number of complete brain connection maps and could lead to a greater understanding of the human brain – one of the motivations for distributing the software as open source. When studying brain connectivity, researchers often already have the raw data needed to complete the map, now they have the program to complete the picture.

By Michael David Mitchell, Sarah Perrin

Contact: Michael David Mitchell, Tel: [+41 21 69] 37022, Email:

Source: Ecole Polytechnique Fédérale de Lausanne (EPFL)

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© 2011 EPFL

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© 2011 EPFL