Course Announcement: Fall 2006
Title: Imaging Brain and Cognition
Call and Course number: 57850 NBHV G4320 NBIO 030

Instructor: Joy Hirsch, Ph.D., Professor
Director, fMRI Research Center
Departments of Radiology and Psychology
Center for Neurobiology and Behavior
Address: Neurological Institute B-41
710 West 168th Street
New York, NY 10032
Phone: 212-342-0291
Fax: 212-342-0855
E-Mail: jh2155@columbia.edu
Website: www.fmri.org
Assistant: Elisa Edmondson
Meeting Times: Wednesdays at 3:00PM - 5:00PM
Neurological Institute, Imaging Conference Room B-43


The Center for Neurobiology and Behavior of Columbia University will offer a one semester course this fall (2006) on “Functional Neuroimaging of Human Brain and Cognition” (3 points) as one of its advanced neurobiology courses. Joy Hirsch will direct the course. The course will be taught as a combined lecture and lab course that will focus on both current topics in neuroimaging and techniques of functional mapping using functional magnetic resonance imaging, fMRI. Functional magnetic resonance imaging extends conventional anatomical imaging to include localization of the brain areas active during perceptions, actions, emotions, and cognitive tasks. The advantages of this new neuroimaging technique offer unprecedented opportunities for the investigation of human brain functional organization as well as medical applications such as neurosurgical planning, drug development, assessment of mood disorders and guiding neuro rehabilitation. However, realization of these advantages requires new experimental methods, analyses, and novel approaches to old questions. A focus of this course will be on the development of creative approaches to the study of human brain functions using fMRI. The multi-disciplinary nature of functional brain mapping provides opportunities for collaborations and interactions between students and faculty with diverse backgrounds including medicine, neuroscience, psychology, computer science, engineering, biophysics, and mathematical modeling. The course material is intended to facilitate interdisciplinary projects and discussions.


Objectives:
The long term goals of this course include gaining a sufficient background in essential principles of imaging and neuroscience to serve as a foundation for future independent investigations.
Specifically the course offers:
- Hands-on experience with fMRI experimental design and data analysis.
- Examples and models of on-going fMRI experiments from Columbia investigators in order to acquaint students with future research options and directions within the University.
- Introduction to clinical and translational neuroimaging projects and models of collaborative neuroimaging investigations.
- Critical skills in evaluation of published neuroimaging studies through discussion of experimental designs, evidence and claims.
Topics will include selected questions in cognition, vision and visual perception, emotion and affect, and clinical and translational applications in order to provide a broad orientation to current standards of practice, creative investigational approaches and limitations to fMRI research. The rationale for the order of the topics in the following outline is to build a knowledge base from the signal to simple, descriptive mapping of single tasks and subjects, to population studies and hypothesis based investigations.
The format of this class will have two parts. The first hour will include either a lecture by a faculty member, guest lecturer, or a presentation of an on-going research project by a Columbia student or post-doc currently engaged in a fMRI research program. The objectives of this course include acquainting students in the class with the faculty and investigators at Columbia with expertise and research interests in fMRI. These investigators and their students and post-docs will present summaries and discussions of their projects to serve as models for creative experimental approaches to complex problems.
The second hour will either be a technical discussion related to an aspect of the experimental design, data analysis, integration of behavioral data, and future directions, or hands on experience with functional imaging.


Course Requirements:
Students (in groups or individually) will select a research question and design an fMRI experiment which will be presented for class discussion and a short paper. The design, run and analyses of results will be organized during the technical discussions. Each student will participate in or give a topic presentation during the course that may include the results of their fMRI project. These presentations and participation in class discussion will form the basis for the grade for those students taking the course for credit. There will be no exams.
The course is open to any graduate student, postdoc, resident or fellow who has taken an introductory neuroscience course. Auditors are welcome and their level of participation is expected to be the same as that of those taking the course for credit, i.e. attend class regularly, participate in discussions, run an experiment and give a presentation. Enrollment will be limited, however, to allow adequate participation by all enrollees.

2006 Course Outline

Class requirements:

                                               2) a class discussion of an assigned reading.

References:
Primary text:



WEEK 1: 6th SEPTEMBER 2006: INTRODUCTION AND COURSE ORGANIZATION
3:00-5:00: NEUROIMAGING AND THE STRUCTURE/FUNCTION PROBLEM: WHERE ARE THE FRONTIERS
* Topics for course projects
* Background reading:
* Savoy, R., History and Future directions of human brain mapping and functional neuroimaging, Acta Psychologica, 2001, 107 (1-3): 9-42. (Available on Courseworks)

WEEK 2: 13th SEPTEMBER 2006
3:00-4:00: INTRO TO SCANNER AND SAFETY (Stephen Dashnaw)
4:00-4:30: INTRO TO PROCEDURES AND PRACTICES FOR fMRI EXPERIMENTS
(Anna Barnes, Ph.D.)
* Protection of human subjects, good clinical practices certification, ethical and regulatory issues.
4:30-6:00: Introduction to theoretical and technical foundations of fMRI (Joy Hirsch, Ph.D.)
6:00-7:00: Safety video and certification
* Readings:
* Huettal
* Chapters 1: An introduction to fMRI
* Chapter 2: MR safety p.39-48
* Chapter 6: From neuronal hemodynamic activity
* Gore, J.C., Principles and practice of functional MRI of the human brain, J. Clin. Invest., 2003, 112: 4-9.
* Savoy, R., Functional Magnetic resonance imaging (fMRI), Encyclopedia of the human brain, 2002, 1-21.
* Logothetis, N.K., Pauls, J., Augath, M., Trinath, T., Oeltermann, A., Neurophysiological investigation of the basis of the fMRI signal, Nature, 2001, 412: 150-157.

Slides from Dr. Hirsch's Lecture on 9/11/2006

WEEK 3: 20th SEPTEMBER 2006
3:00-5:00: PRINCIPALS OF PHYSICS THAT ENABLE MRI AND fMRI (Alayar Kangarloo, Ph.D.)
5:00-7:00: TBD
* Readings (Others may be added):
* Huettel:
* Chapter 2: How MR scanners work, p.27-39
* Chapter 3: Basic principles of MR signal generation
* Chapter 5: MR contrast mechanisms and pulse sequences
* Review Chapter 6: Basic principles of MR signal formation

WEEK 4: 27th SEPTEMBER 2006
3:00-5:00 EXPERIMENTAL DESIGN AND IMAGE ANALYSIS: (Martina Pavlicova, Ph.D.)
5:30-7:00: Lab
* INTRODUCTION TO SPM: “HANDS ON” COMPUTATIONAL DEMO
(Anna Barnes, Ph.D.)
* A “recommended” design
* Reading (Others may be added):
* Huettel:
* Chapter 10: Pre-processing of fMRI data
* Chapter 11: Experimental design
* Chapter 12: Statistical analysis
* Savoy, R., Using small numbers of subjects in fMRI-based research, IEEE Engineering in Medicine and Biology Magazine, 2006, March/April: 52-59.

WEEK 5: 4th OCTOBER 2006
3:00-4:30: THE VISUAL SYSTEM AS A MODEL FOR FUNCTIONAL IMAGING. FUNCTIONAL SPECIFICITIES FOR CASES, PLACES, AND OBJECTS. RETINOTOPIC MAPPING, (Joy Hirsch, Ph.D.)
4:30-5:00: Retinotopic mapping (John Ferrera)
5:30-6:30: Visualization: John Ferrera and Xian Zhang, Ph.D. discussion
* Readings: Assigned for discussion
* Halgrem E., Dale, A.M., Sereno, M.I., Tootell, R.B.H., Marinkovic, K., Rosen, B.R., Location of human face-selective cortex with respect to retinotopic areas, Human Brain Mapping, 7: 29-37, 1999.
* Savoy, R., Experimental design in brain activation MRI: Cautionary tales, Brain Research Bulletin, 2005, 67: 361-367.
* Grill-Spector, K., Kushnir, T., Hendler, T., Edelman, S., Itzchak, Y., Malach, R., A sequence of object-processing stages revealed by fMRI in the human occipital lobe, Human Brain Mapping, 6: 316-328, 1998.
* Engel, S.A., Glover, G.H., Wandell, B.A., Retinotopic organization in human visual cortex and the spatial precision of functional MRI, Cerebral Cortex, 7: 181-192, 1997.
* Tootell, R.B.H., Reppas, J.B., Kwong, K.k., Malach, R., Born, R.T., Brady, T.J., Rosen, B.R., Belliveau, J.W., Functional analysis of human MT and related visual cortical areas using magnetic resonance imaging, J. of Neuroscience, 1995, 15 (4): 3215-3230.
* Kanwisher, N., McDermott, J., Chun, M.M., The fusiform face area: a module in human extrastriate cortex specialized for face perception, J. Neuroscience, 1997, 17 (11): 4302-4311.
* Summerfield, C., Egner, T., Mangels, J., Hirsch, J., Mistaking a House for a Face: Neural Correlates of Misperception in Healthy Humans, In Press (Advance Access, July 13, 2005), Cerebral Cortex, 2005.
* Warnking, J., Dojat, M, Guerin-Dugue, A., Delon-Martin, C., Olympieff, S., Richard, N., Chehikian, A., Segebarth, C., fMRI retinotopic mapping-step by step, NeuroImage, 2002, 17: 1665-1683.

WEEK 6: 11th OCTOBER 2006
3:00- 7:00: NEUROIMAGING AS A BASIS FOR THEORIES OF COGNITIVE PROCESSES:
Robert Savoy, Ph.D.
* Technical discussion: Data processing; General linear model
* Readings:
* Chapter 14: Advanced methods
* Chapter 15: Converging operations
* Lab: Discussion of class projects

Greene et al, An fMRI Analysis of the Human Hippocampus: Inference, Context and Task Awareness

David B. Cox and Robert Savoy, Functional magnetic resonance imaging (fMRI) Òbrain readingÓ: detecting and classifying distributed patterns of fMRI activity in human visual cortex

K.M. O'Crave and N. Kanwisher, Mental Imagery of Faces and Places Activates Corresponding Stimulus-Specific Brain Regions
K.M. O'Craven, Paul E. Downing, Nancy Kanwisher, fMRI Evidence for Objects as the units of attentional selection
K.M. O'Craven, B.R. Rosen, K. Kwong, A. Treisman, and R. Savoy, VoluntaryAttentionModulatesfMRIActivity in Human MT-MST

WEEK 7: 18th OCTOBER 2006
3:00- 7:00:     BRAIN LABELING
Arno Klein, Ph.D.
http://www.binarybottle.com/links/brain_links.html
this is a good overview of brain atlases and their uses (toga & thompson):
http://www.loni.ucla.edu/~thompson/whole_atlas.html

* Reading (Others may be added):
* Klein, A., Hirsch, J., Mindboggle:  A scatterbrained approach to automate brain labeling, Vol 24, 261-280, NeuroImage, 2005.
* Huettel Review Chapter 15
* Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain, Neuron, Volume 33, Issue 3, 31 January 2002, Pages 341-355
* Bruce Fischl , David H. Salat , Evelina Busa , Marilyn Albert , Megan Dieterich , Christian Haselgrove , Andre van der Kouwe , Ron Killiany , David Kennedy , Shuna Klaveness et al.
* Neuroimage
* Neurol Med Chir (Tokyo) 45, January, 2005
* Animal & Insect

WEEK 8: 25th OCTOBER 2006
3:00-4:30: NEURAL FOUNDATIONS OF DECISION MAKING (Jack Grinband, Ph.D.)
* Lab: Class projects/data collection
* Reading (Others may be added):
* Grinband, J., Hirsch, J., Ferrera, V.P., A neural representation of categorization uncertainty in the human brain, Neuron, 49: 757-763, 2006.
* Platt, M., Glimcher, P., Neural correlates of decision variables in parietal cortex, Nature, 400: 233-239, 1991.

WEEK 9: 1st NOVEMBER 2006
3:00-5:00: FUNCTIONAL IMAGING OF NEUROCIRCUITRY RELATED TO SPATIAL ATTENTION AND COGNITIVE CONTROL (Tobias Egner, Ph.D.)
* Technical discussion: Data analysis techniques- threshold/GLM/SPM2/Brain Voyager/FSL visualization strategies
* Lab: Class projects/data collection and/or analysis
* Reading(Others may be added) :
* Egner, T., Hirsch, J., Cognitive control mechanisms resolve conflict through cortical amplification of Task-Relevant information, 8 (12), 1784-1790, Nature Neuroscience, 2005.
* Nieuwenhuis, S., Yeung, N., Neural mechanisms of attention and control: losing our inhibitions?, News & Views, Nature Neuroscience, 2005, 8 (12), 1631-1633.
* Etkin, A., Egner, T., Peraza, D.M., Kandel, E.R., Hirsch, J., Resolving emotional conflict: a model for amygdalar modulation by the rostral anterior cingulate cortex, Neuron, in press, 2006
* Nuñez, J.M., Casey, B. J., Egner, T., Hare, T., Hirsch, J., Intentional False Responding Shares Neural Substrates With Response Conflict and Cognitive Control, Vol 25, 267-277, NeuroImage, 2005.
*Yantis, S., Serences, J.T. (2003). Cortical mechanisms of space-basedand object-based attentional control. Current Opinion in Neurobiology 13, 187-193.
*Pessoa, L., Kastner, S., Ungerleider, L.G. (2003). Neuroimaging studies of attention: from modulation of sensory processing to top-down control. Journal of Neuroscience 23, 3990-3998.



WEEK 10: 8th NOVEMBER 2006
3:00-5:00:       THE NEUROBIOLOGY OF EMOTION AND ANXIETY - Joy Hirsch, Ph.D.

                                           Platt, et al         (Albert Lin)

                                          Moffitt, et al     ( Spiro Pantazatos)

WEEK 11: 15th NOVEMBER 2006

3:00-5:00:       STUDENT PAPER PRESENTATIONS

Crinion, J., Turner, R., Grogan, A., Hanakawa, T., Noppeney, U., Devlin, J.T., Aso, T., Urayama, S., Fukuyama, H., Stockton, J., Usui, K., Green, D.W., Price, C.J., Language Control in the Bilingual Brain, Science (vol. 312, no. 5779, 1537-1540), 2006.

.

WEEK 12: 22nd NOVEMBER 2006 -**CLASS CANCELLED (THANKSGIVING)
3:00-5:00:       

WEEK 13: 29th NOVEMBER 2006
3:00-5:00:       (Joy Hirsch, Ph.D.)

 WEEK 14: 6th DECEMBER 2006 (Last Class)
3:00-7:00:       

Other References:

McCabe, K., Houser, D., Ryan, L., Smith, V., Trouard, T., A functional imaging study of cooperation in two-person reciprocal exchange, PNAS, 98, 11832-11835.



WEEK 15: 13th DECEMBER 2006
3:00-7:00: Student presentations – TBA

Other References:
McCabe, K., Houser, D., Ryan, L., Smith, V., Trouard, T., A functional imaging study of cooperation in two-person reciprocal exchange, PNAS, 98, 11832-11835.