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.
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
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.
*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.
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
.
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.