The brain is perhaps the most fascinating of all organs in the human body, as it is the foundation of human thought and behavior. Despite the explosion of brain research that has occurred over the past several years, the brain remains mysterious with many unknowns. Moreover, with the 12 month prevalence of mental illness being about 1 in 5 adults worldwide and 29.2% across lifetime (Steel et al., 2014), a better understanding of this system would likely lead to better methods of support and treatment for this population.

Throughout history the ability to study the brain has been limited due to lack of technology. Over the past two decades however, a technique called functional Magnetic Resonance Imaging (fMRI) has led to the ability to study a living brain non-invasively and thus has become extremely popular among researchers. As fMRI requires some knowledge of physics, neuroscience, psychology, and statistics, it is an area which typically requires interdisciplinary teams to work together to fully understand the methods and to make proper inferences about the results. Furthermore, while it has advanced our understanding of the brain, its limitations and potential methods to overcome or minimize these limitations should also be considered.

This course offers a detailed introduction to fMRI, starting with an overview of neuroscience and neuroanatomy and advancing to the functionality of the brain. Initially, a brief history of past and current techniques to study this functionality will be described, leading into a detailed introduction to MRI and fMRI.

The second half of the course focuses on the theory and application of both MRI and fMRI. Principles of magnetic resonance and their application to imaging are covered, as well as how MRI progressed from a measure of structure to a measure of function. Practical applications, such as design of experiments, preprocessing, and analysis of data as well as limitations of these methods are also covered.

Finally, the course offers an overview of how fMRI is used to study functional connectivity in the brain, and a brief introduction to diffusion tensor imaging, which is applied to study white matter tracks in the brain, is given. The final two lectures will be spent on current applications of fMRI to study cutting edge topics such as the processing of emotions, learning and memory, fear learning and extinction, and the effects of sleep.

The course is designed for students with little or no background in neuroscience and imaging, although a basic background in biology and physics is highly preferred. Thus, the course is suitable for undergraduate students, graduate students, and other professionals with an interest in the brain.


Course Objectives
  • Develop a basic understanding of the brain and the nervous system.
  • Learn about the types of functional neuroimaging and their limitations.
  • Gain an understanding of MRI and fMRI and their potential uses.
  • Develop an understanding of the challenges and limitations of fMRI.
  • Explore some current applications of fMRI in neuroimaging research.

Tentative Schedule of Classes

The date/time in the schedule below are fixed. Topics/content/order of presentation may change marginally depending on the audience.

Date/Time Topic
7/11/2016
0900-0930
Inauguration by the Vice Chancellor, followed by tea and snacks.
7/11/2016
1000-1100
Brief Introduction to neuroscience: Broad overview of the field including its origins to main topics in research today.
7/11/2016
1115-1215
The nervous system, anatomy and physiology at the cellular level, cell types, communication between cells and how they work together to contribute to the functioning of the brain as a whole.
8/11/2016
0930-1030
Overall anatomy of the brain, the architecture of the different lobes, the layers of the cerebral cortex, terminology used to describe and study different regions.
8/11/2016
1100-1200
Mapping function to structure: Functional organization of the brain, how different regions specialize and work together to control our behavior (emotions, executive functioning, etc.).
9/11/2016
0930-1030
Introduction to anatomical and functional imaging, how the methods have progressed our understanding of the brain.
9/11/2016
1100-1200
Overview of the types of neuroimaging: Direct measures of neural activity (Evoked potentials, EEG, MEG); indirect measures of neural activity (PET imaging, functional MRI).
10/11/2016
0930-1030
Magnetic Resonance Imaging: History, advantages to research, basic principles of magnetic resonance.
10/11/2016
1100-1200
MRI continued: Acquisition of MR images - parameters in MRI, spin density, contrasts, spatial orientation, imaging other elements besides hydrogen.
10/11/2016
1200-1300
Tutorial cum assisted self-study and discussion session.
11/11/2016
0930-1030
Functional Magnetic Resonance Imaging: How it works, the BOLD signal, what is measured and the information it offers.
11/11/2016
1100-1200
fMRI in Practice: Design of experiments, raw data, preprocessing the data, first and second level analysis.
14/11/2016 Public Holiday: No Classes
15/11/2016
0930-1030
Statistical problems of fMRI: Sources of variability that negatively affect the experiment (motion, physiological noise, field distortions) and how to control for/minimize these.
15/11/2016
1045-1145
Modeling the fMRI data: The general linear model for individual analysis, techniques to combine groups of subjects and problems of multiple comparisons.
15/11/2016
1200-1300
Mini-lab session: Students design their own fMRI study, discussion.
16/11/2016
0930-1030
MRI/fMRI Safety: Risks of MRI and safety precautions.
16/11/2016
1045-1145
fMRI to study functional connectivity and "resting state" fMRI.
16/11/2016
1200-1300
Diffusion Tensor Imaging – an MRI method to study white matter tracks.
17/11/2016
0930-1030
Specific application of fMRI: Emotion processing, learning and memory.
17/11/2016
1045-1145
Specific applications of fMRI continued: PTSD, Fear learning and extinction, and the effects of sleep.
17/11/2016
1200-1330
Examination/Assessment/Evaluation. Venue: Kelkar Laboratory, Centre for Modeling and Simulation, SPPU
18/11/2016
0930-1030
Specific applications of fMRI continued: Potential clinical application followed by overview discussion of the course, interactive question-and-answer session, discussion of exam problems, etc..
18/11/2016
1100-1200
Concluding session.
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