SDSU Foundations of Neuroimaging (PSY 596 — Fall 2017)


Marty Sereno -- email: msereno - AT - sdsu
time: MWF 1:00 - 1:50 AM (graduate: TBA)
location: SSW 2667 (Learning Glass Studio, Student Services West)

Required Readings:
Huettel, S., A.W. Song, and G. McCarthy (2014) Functional Magnetic Resonance Imaging, 3rd ed.
Sereno Lecture Notes (69-page PDF [11MB, updated: Mar 2016] -- single-page links below)

Recommended Readings:
Additional books/articles below

Homework #1 (due ##/##/##, paper printout, incl. code and graphs)
Homework #2 (due ##/##/##, paper printout, incl. code and graphs, brain image is here)
Final Paper: 10 page literature review on narrow methodological topic (start search in
    Magnetic Resonance in Medicine, Neuroimage, Human Brain Mapping)

Learning Objectives:
Students will be able to do the following:
   (1) explain excitation/recording/contrast of magnetic resonance signals and echoes using the Bloch equation
   (2) compute Fourier transform, use it to explain how RF stimulation, gradients, and RF coil signals generate brain images
   (3) describe origin/localization of EEG/MEG signals, cortical surface-based methods, and how to combine them w/fMRI
   N.B.: consult with me if a disability hinders your performance so we can use University resources to maximize learning

Description and Prerequisites:

Lecture Topics -- Fall 2017 -- this page:

Week 1 -- MRI Signals I -- Huettel Chap. 2,3 (Buxton Chap. 3,4,6,7)

Week 2 -- MRI Signals II -- Huettel Chap. 5,9 (Buxton Chap. 4,8)

Week 3 -- Fourier Transform, Slice Selection -- Huettel Chap. 4 (Buxton Chap. 5,10)

Week 4 -- MRI Image Formation -- Huettel Chap. 4 (Buxton Chap. 5,10)

Week 5 -- Image Reconstruction, Structural Pulse Sequences -- Huettel Chap. 4 (Buxton Chap. 11)

Week 6 -- Functional MRI, Artifacts, Correction -- Huettel Chap. 6,7,8,10 (Buxton Chap. 12,16,17)

Week 7 -- Diffusion and Perfusion, General Linear Model -- Huettel Chap. 11, 12 (Buxton Chap. 9, 15)

Week 8 -- Surface-Based Methods and Cortical Mapping -- Online PDFs

Week 9 -- Sources of EEG/MEG -- Huettel Chap. 15, Online PDFs

Week 10 -- EEG/MEG Localization -- Online PDFs


Math Resources:

Free Software:
FreeSurfer (MGH)
FreeSurfer (retinotopy-enabled) -- contact msereno at ucsd edu

Web MRI Resources:
Hornak, J.P. (1996-2002) The Basics of MRI
D.M. Higgins (2006) K-space Tool
Jody Culham (2002) fMRI for Dummies
Carl D. Gregory (1998) MRI Artifact Gallery

Neuroimaging Books:
Buxton, R. (2009) Introduction to Functional Magnetic Resonance Imaging, 2nd ed.
Huettel, S., A.W. Song, and G. McCarthy, 3rd ed. (2014) Functional Magnetic Resonance Imaging
Haacke, E.M., R.W. Brown, M.R. Thompson, and R. Venkatesan (1999) Magnetic Resonance Imaging
Bernstein, M.A., K.F. King, and X.J. Zhou (2004) Handbook of MRI Pulse Sequences
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., W.G. Bradley, C.J. Lisanti (2004) MRI: The Basics
Nunez, P.L (1981) Electric Fields of the Brain

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:
Turbo ASL
Spherical Navigators
Inverse Method Distortion Correction
Point-Spread Function Mapping Distortion Correction

MRI Data Analysis Papers:
Estimation, and Predictability
Detection, Estimation, and Predictability

Visual Mapping Papers:
Analysis of Retinotopy
Human Visual Areas
Visual Mapping Review '98
Visual Mapping Review '05
Retinotopy Step-by-Step
Human V1
Human V3A
Ipsilateral Representation
Human V4
Human V6
Human V7
Human V8
Human MT/MST
Human LIP
Human VIP Multisensory
Visual Tracking
Frontal Maps

Auditory Mapping Papers:
Auditory Phase-Map

Somatosensory Mapping Papers:
Somatosensory 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: May 5, 2017
Scanned class notes (links above) © 2017 Martin I. Sereno.
Don't redistribute notes without attribution and link to this page.
Supported by NSF 0224321, NIH MH081990, Royal Society Wolfson.