Introduction
Magnetic resonance imaging (MRI) has been playing a vital role to study brain anatomy and functions and their abnormalities. MRI is non-invasive and can create various contrasts to study different types of brain tissues and functions. Using diffusion MRI, one can study the diffusion properties of water molecules in brain tissues. This allows us to track white matter fibers and create a complete map of the brain fiber tracks, a process that is called Tractography. Through advanced segmentation techniques, gray matter regions can be segmented to different brain structures well-known to neurologist. Intersecting generated fiber tracts with segmented gray matter results into brain networks or connectome. Studying connectomes help analyzing changings occurring to the brain structure due to the onset of different diseases.
CoNECt
CoNECt stands for "The Collaborative Neuroimaging Environment for Connectomics". It is an open source diffusion MRI analysis tool. CoNECt is able to generate full brain tractography using two different models:
- Diffusion Tensor Imaging (DTI)
- Tensor Distribution Function
Supported imaging files: Analyze, NIFTI, raw Supported tractography files: DTI Studio, CoNECt
CoNECt also contains functionalities for generating, analyzing and visualizing connectomes or brain networks using various graph theoretic metrics.
History
It was the first software developed in the CoNECt lab. The lab was formed as collaboration between various departments at the University of Illinois at Chicago. For more information about the CoNECt lab, please check http://conect.brain.uic.edu/. CoNECt was part of my PhD research in the joint research between the ECE and psychiatry departments.
Compilation
In order to compile CoNECt, the following libraries are required:
- VTK 5.6 http://www.vtk.org/download/
- armadillo http://arma.sourceforge.net/
- Lapack and BLAS (included with armadillo)