Neuroscience Research


We collaborate with Prof. Strother’s  research group from Rotman Research Institue, Baycrest, and explore the following aspects in neuroscience related projects.

  1. Bullet Explore more refined fMRI image registration through the AFNI package.

  1. Bullet Deployment of the DTI pipeline packaged as VM appliance onto our cluster.

  1. Bullet Exploring existing and alternative solutions for high dimensional space exploration.


Neuroscience Projects


Ali Hashemi

Bogdan Simion

Francesca Sarzetto

Jeff Cassidy

Jin Chen

Prof. Amza

Ricky Tong

Prof. Strother


[1] A. Krishnan, L. J. Williams, A. R. McIntosh, and H. Abdi, "Partial Least Squares (PLS) methods for neuroimaging: A tutorial and review," NeuroImage, vol. 56, no. 2, pp. 455-475, 2011.

[2] T. Schmah, G. Yourganov, R. S. Zemel, G. E. Hinton, S. L. Small, and S. C. Strother, "Comparing Classification Methods for Longitudinal fMRI Studies," Neural Computation, vol. 22, no. 11, pp. 2729-2762, 2010.

[3] S. Strother, A. Oder, R. Spring, and C. Grady, "The NPAIRS Computational Statistics Framework for Data Analysis in Neuroimaging," in 19th International Conference Computational Statistics, Paris, France, 2010, pp. 111-120.

[4] S. C. Strother, "Evaluating fMRI preprocessing pipelines," IEEE Engineering in Medicine and Biology Magazine, vol. 25, no. 2, pp. 27-41, 2006.


The preprocessing steps interact with virtually every decision made in designing and performing fMRI experiment.

Magnetic Resonance Imaging (MRI) is a medical imaging technique based on some physical properties of the matter. Every molecule immersed in a magnetic field aligns with the field itself, and when excited by radio frequency impulses it changes its angle, and then returns to the aligned state. The energy released during this last phase is collected, encoded by gradient magnetic fields to reconstruct the 3D position of the originating point. The molecules most frequently used for this purpose are water molecules, and the more they are present in the examined tissues, the stronger the signal emitted, therefore providing contrast.

Functional MRI (fMRI) studies the changes in the tissues over time, examining for example blood-oxygenation level-dependent (BOLD) contrast, since active areas of the brain consume more oxygen, and by analyzing the reduction of oxygen in the blood it is possible to estimate which areas are more active.

By carefully planning different kinds of magnetic fields and their impulses, it is also possible to analyze the movement of molecules within the brain through diffusion. Every molecule in fact tends to move randomly in the directions, unless its movement is restricted, so that they move more quickly in one direction than the others. This is the case in the white matter of the brain, with movements happening mainly along the direction of the neuron's axon, a long ramification of these cells connecting different areas of the nervous system. Diffusion Tensor Imaging (DTI) highlights these movements, examining the integrity of the axon connections in the white matter of the brain.

fMRI and DTI