Cognitive Science 276 -- Neuroimaging (Fall 2005)
FALL 2005 (current/latest version:
here)
Professor:
Marty Sereno
class time -- Mon/Wed/Fri 10:00-11:00, room change: CSB 272 (was CSB 180!)
Required Readings:
Buxton, R. (2002) Introduction to Functional Magnetic Resonance Imaging, 1st ed. [2nd ed. not ready yet -- due mid 2006]
Sereno Lecture Notes (62-page PDF [9MB, last update: 11/23/04] -- print 10-20 pages at a time,
or use single-page links below)
[N.B.: PDF currently complete only to 8th week -- 15 pages to be added]
Additional journal articles:
below
Assignments:
Homework #1
(due 10/17/05, paper printout, incl. code and graphs)
Homework #2
(due 10/31/05, paper printout, incl. code and graphs, brain image is
here )
Homework #3
(tentatively due 11/21/05, paper printout, incl. code and graphs)
Final Paper: literature review on narrow methodological topic (10 pages, start search in Magnetic Resonance in Medicine, Neuroimage, Human Brain Mapping)
Description and Prerequisites:
This course is an introduction to structural and functional MRI,
fMRI time series analysis, cortical-surface based data analysis, and
the neural basis, recording, and localization of EEG and MEG signals.
Although this course does not require a background in linear algebra,
electromagnetism, and the Fourier transform, students will be expected
to develop a solid grasp of the key equations underlying the different
neuroimaging methods. There are two other neuroimaging courses. The
first (Bioengineering
280A -- Principles of Biomedical Imaging, Fall 2005 syllabus) is
taught by Tom Liu (another member of the UCSD fMRI center) and provides
a stronger mathematical foundation in the fundamentals of the Fourier
transform and linear systems theory, and covers ultrasound and CT in
addition to MRI. The second is a new team-taught three-quarter sequence
that will be offered by the Radiology Department. The first quarter of
this sequence has been moved the Winter 2006 (originally planned for
Fall 2005) and will be headed up by David Dubowitz who is also at the
UCSD fMRI Center.
Lecture Topics (weeks 7-10 under revision): Fall 2005 -- this page:
http://cogsci.ucsd.edu/~sereno/276/
First class -- Fri, Sept 23, 10:00 AM, CSB 180 Buxton Chap. 3, 6
- Introduction to Neuroimaging -- MRI, fMRI, EEG, MEG
- MRI hardware
Week of 9/26 -- MRI Signals I -- Buxton Chap. 4, 7
Week of 10/3 -- MRI Signals II -- Buxton Chap. 4, 8
Week of 10/10 -- Fourier Transform, Slice Selection -- Buxton Chap. 5, 10
Week of 10/17 -- MRI Image Formation -- Buxton Chap. 5, 10
Week of 10/24 -- Image Reconstruction, Structural Pulse Sequences -- Buxton Chap. 11
Week of 10/31 -- Functional MRI, Artifacts, Correction -- Buxton Chap. 12, 16, 17
Week of 11/7 -- Diffusion and Perfusion, General Linear Model -- Buxton Chap. 9, 15
Week of 11/14 -- Surface-Based Methods and Cortical Mapping -- Cortical Surface & Visual Mapping PDFs
Week of 11/21 -- Sources of EEG/MEG
Week of 11/28 -- EEG/MEG Localization
READINGS
Math Resources:
MATLAB Primer
Free Software:
FreeSurfer (MGH)
FreeSurfer (UCSD retinotopy-enabled)
AFNI
FSL
SPM2
Web MRI Resources:
Hornak, J.P. (1996-2002) The Basics of MRI
Charles Mistretta (1998) A Traveler's Guide to K-Space
Jody Culham (2002) fMRI for Dummies
Carl D. Gregory (1998) MRI Artifact Gallery
Neuroimaging Books:
Buxton, R. (2002) Introduction to Functional Magnetic Resonance Imaging
Huettel, S., A.W. Song, and G. McCarthy (2004) Functional Magnetic Resonance Imaging
Haacke, E.M., R.W. Brown, M.R. Thompson, and R. Venkatesan (1999) Magnetic Resonance Imaging
Liang, Z-P. and P.C Lauterbur (1999) Principles of Magnetic Resonance Imaging
Nishimura, D.G. (1996) Principles of Magnetic Resonance Imaging [available from author]
Hashemi, R.H. and W.G. Bradley (1997) MRI: The Basics
Nunez, P.L (1981) Electric Fields of the Brain
Background:
Bracewell, R.N. (2000) The Fourier Transform and its Applications
Oppenheim, A.V. and A.S. Willsky (1997) Signals and Systems
Karu, Z.Z. (1995) Signals and Systems Made Ridiculously Easy
Wangsness, R.K. (1986) Electromagnetic Fields
Greenberg, M.D. (1978) Foundations of Applied Mathematics
Koch, C. and I. Segev (1998) Methods in Neuronal Modeling
Johnston, D. and S.M.-S. Wu (1995) Foundations of Cellular Neurophysiology
[updates of following papers in progress]
Pulse Sequence Papers:
QUIPSS II
Turbo ASL
Spherical Navigators
SENSE
SPACE RIP
Inverse Method Distortion Correction
Point-Spread Function Mapping Distortion Correction
MRI Data Analysis Papers:
Estimation, and Predictability
Detection, Estimation, and Predictability
3dDeconvolve
Visual Mapping Papers:
Analysis of Retinotopy
Human Visual Areas
Visual Mapping Review
Retinotopy Step-by-Step
Human V1
Human V3A
Ipsilateral Representation
Human V4
Human V7
Human V8
Human MT/MST
Human LIP Map
Visual Tracking
Auditory Mapping Papers:
Auditory Phase-Map
Dale and Sereno, 93:(cortical surface, EEG/MEG inverse)
manuscript (equations more readable), or
journal scan
Cortical Surface Reconstruction Papers:
Segmentation and Reconstruction
Inflation, Flattening, Coordinates
Inter-Subject Morphing
Cortical Thickness
Topology Repair
Montreal Cortical Surface Method
Van Essen Surface-Based Atlas
EEG and MEG Localization Papers:
fMRI/EEG Attention
Noise Sensitivity Normalized Inverse--Data
Noise Sensitivity Normalized Inverse--Models
Mapping the Conductivity Tensor
N400 Localization
Intracortical EEG Papers:
Surface Plus Laminar Analysis
3D CSD of Rat BAER
last modified: September 23, 2005
Scanned class notes (links above) © 2005 Martin I. Sereno.
Don't redistribute without attribution and link to this page.
Supported by NSF 0224321.
