Cognitive Science 276 -- Neuroimaging (Fall 2004)
FALL 2004 (current/latest version:
here)
Professor:
Marty Sereno
class time -- Mon/Wed/Fri 10:00-11:00 AM, CSB 180
Required Readings:
Buxton, R. (2001) Introduction to Functional Magnetic Resonance Imaging
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 10/18/04, paper printout, incl. code and graphs)
Homework #2
(due 11/17/04, paper printout, incl. code and graphs, brain image
here )
Final Paper: literature review on narrow methodological topic (10 pages, start search in Magnetic Resonance in Medicine, Neuroimage)
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, the goal is to develop an intuitive grasp
of the key equations underlying the different neuroimaging methods.
There is another imaging course
(Bioengineering
280A -- Principles of Biomedical Imaging) taught by Tom Liu (another
member of the UCSD fMRI center). That course 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.
Lecture Topics: Fall 2004 -- this page:
http://cogsci.ucsd.edu/~sereno/276/
First class -- Fri, Sept 24, 10:00 AM, CSB 180 Buxton Chap. 3, 6
- Introduction to Neuroimaging -- MRI, fMRI, EEG, MEG
- MRI hardware
Week of 9/27 -- MRI Signals I -- Buxton Chap. 4, 7
Week of 10/4 -- MRI Signals II -- Buxton Chap. 4, 8
Week of 10/11 -- Fourier Transform, Slice Selection -- Buxton Chap. 5, 10
Week of 10/18 -- MRI Image Formation -- Buxton Chap. 5, 10
Week of 10/25 -- Image Reconstruction, Structural Pulse Sequences -- Buxton Chap. 11
Week of 11/1 -- Functional MRI, Artifacts, Correction -- Buxton Chap. 12, 16, 17
Week of 11/8 -- Diffusion and Perfusion, General Linear Model -- Buxton Chap. 9, 15
Week of 11/15 -- Surface-Based Methods and Cortical Mapping -- Cortical Surface & Visual Mapping PDFs
Week of 11/22 -- Sources of EEG/MEG
Week of 11/29 -- EEG/MEG Localization
READINGS
Math Resources:
MATLAB Primer
Software:
UCSD Retinotopy-enabled FreeSurfer
Web Courses:
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
MRI Books:
Buxton, R. (2002) Introduction to Functional Magnetic Resonance Imaging
Haacke, E.M., R.W. Brown, M.R. Thompson, and R. Venkatesan (1999) Magnetic Resonance Imaging
Hashemi, R.H. and W.G. Bradley (1997) MRI: The Basics
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)
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 21, 2004
Scanned class notes (links above) © 2004 Martin I. Sereno.
Don't redistribute without attribution and link to this page.
Supported by NSF 0224321.
