COL 786: Advanced Functional Brain Imaging
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Week Number |
Topics to be covered |
References |
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1 |
Introduction to the course and nervous system |
o Principles of Neural Science, 4th Edition by Eric Kandel, James Schwartz and Thomas Jessell, Chapter 2 o At coursera.org Medical Neuroscience by Leonard E. White, Units 1-2 and 1-3 o Chapter 1 of Clinical Neuroanatomy Seventh Edition, by Richard S. Snell. o TED Talk-- Vilayanur Ramachandran: The neurons that shaped civilization |
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2 |
Basic neuroanatomy, introduction to FSL |
o Medical Neuroscience, Units 1-1 and 1-4 to 1-9 o MIT Introduction to Neuroanatomy Series (parts 1-6) o TED talk: A map of the brain o TED talk by Miguel Nicolelis, A monkey that controls a robot with its thoughts |
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3 |
MRI imaging basics |
o Paul Callaghan Videos on MRI o MRI Physics for Biomedical Researchers, Book By Gordon E. Sarty, Chapters 1, 5, 7, 8 and 14 |
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4-5 |
fMRI basics -- Protocol design, fMRI processing pipeline and details |
o TED talk: A neural portrait of the human mind o Principles of fMRI 1 and 2 course by Johns Hopkins University at coursera.org o Uludag, Kâmil, David J. Dubowitz, and Richard B. Buxton. "Basic principles of functional MRI." Clinical MRI. Elsevier, San Diego (2005): 249-287. |
|
6 |
Introduction to statistics, formal notations |
o Introduction to the Science of Statistics, by Joseph C. Watkins. Chapters 12, 14, 16, 17 |
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7-8 |
GLM statistics, multi-subject statistics, Multiple comparison problem, Bonferroni correction, FDR correction |
o Lazar, Nicole. The statistical analysis of functional MRI data. Springer Science & Business Media, 2008. , , |
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9 |
Connectivity analysis and statistics |
o Raichle, Marcus E., and Abraham Z. Snyder. "A default mode of brain function: a brief history of an evolving idea." Neuroimage 37.4 (2007): 1083-1090. o Van Den Heuvel, Martijn P., and Hilleke E. Hulshoff Pol. "Exploring the brain network: a review on resting-state fMRI functional connectivity." European Neuropsychopharmacology 20.8 (2010): 519-534. |
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10 |
ISC analysis and statistics |
o Kauppi, Jukka-Pekka, Juha Pajula, and Jussi Tohka. "A versatile software package for inter-subject correlation based analyses of fMRI." Frontiers in neuroinformatics 8 (2015). o Pajula, Juha, Jukka-Pekka Kauppi, and Jussi Tohka. "Inter-subject correlation in fMRI: method validation against stimulus-model based analysis." PloS one 7.8 (2012): e41196. o Hasson, Uri, et al. "Neurocinematics: The neuroscience of film." Projections 2.1 (2008): 1-26. |
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11-12 |
Multi-voxel pattern analysis and brain dynamics using fMRI |
o Norman, Kenneth A., et al. "Beyond mind-reading: multi-voxel pattern analysis of fMRI data." Trends in cognitive sciences 10.9 (2006): 424-430. o Kay, Kendrick N., et al. "Identifying natural images from human brain activity." Nature 452.7185 (2008): 352-355. o TED talk: Could future devices read images from our brains? o Nishimoto, Shinji, et al. "Reconstructing visual experiences from brain activity evoked by natural movies." Current Biology 21.19 (2011): 1641-1646. |
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13-14 |
Other concepts in Neuroscience and project presentations |
o The Secret Life of the Brain, PBS Documentary (all six episodes) o The Man With The 7 Second Memory ITV1 Documentary o The Woman Who Could Not Forget o PBS NOVA Documentary – Memory Hackers |
· Exams — 40 (Minors — 20, Majors — 20)
· Assignments, project — 45 (Assignments — 30, Project — 15)
· Quizzes/home work/class participation — 15