Principles of Neuroimaging B - 2011

Principles of Neuroimaging B, Winter, 2010 - Class Schedule and Syllabus

Main course page for Principles of Neuroimaging (2010-11)

M284A Principles of Neuroimaging A

• Notes for Instructors

Lecture Videos

• Friday 1-3-11 - MR Signals and Contrast, Speaker Mark Cohen
• Wednesday 1-5-11 - MR Spatial Encoding I, Speaker Mark Cohen
• Wednesday 1-5-11 - MR Spatial Encoding II, Speaker Mark Cohen
• Friday 1-10-11 - fMRI and Diffusion, Speaker Mark Cohen
• Wednesday 1-12-11 - fMRI Image Quality and Artifacts, Speaker Mark Cohen
• Friday 1-24-11 - Experimental Design I, Speaker Susan Bookheimer
• Friday 1-24-11 - Experimental Design II, Speaker Susan Bookheimer
• Wednesday 1-26-11 - DTI, Speaker Nathan Hageman
• Friday 1-31-11 - MEG/EEG, Speaker Gregory Simpson
• Wednesday 2-2-11 - Ultra Low Field MRI, Speaker Konstantin Penanen
• Wednesday 2-9-11 - TMS, Speaker Allan Wu
• Friday 2-14-11 - MRS, Speaker Jeff Algers

Week 1 Magnetic Resonance Imaging

Magnetic Resonance Imaging (MRI) is probably the most influential and most felxible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies

Wednesday 1/4/12 - MRI. Speaker: Cohen

OUTLINE Required Readings

• MRI Slides
• These notes by Joseph Hornak are highly professional and complete coverage of MRI.
• eMRI is another excellent online MRI learning resource
• Erwin Hahn - Spin Echoes: Essential reading for the MRI community

above: Figure 1 from Hahn, 1950

Suggested Further Reading

File:PSatSeq.jpg

Friday 1/6/12 - MRI II. Speaker: Cohen

OUTLINE Required Readings

• MRI Slides (same as 1/4/12)

Suggested Further Reading

• READING

• Problem Set 1

WEEKLY SUMMARY

Week 2 MRI Applications

Wednesday 1/11/12 - Diffusion. Speaker: Jeffry Alger

OUTLINE

File:Bandwidth.jpg

Required Readings

Suggested Further Reading

• READING

==Friday 1/13/12 - fMRI. Speaker: Cohen== OUTLINE Required Readings

• slides (same as 1/3/12)

Suggested Further Reading

• READING

Week 3 Advanced MRI Applications and Sequences

==Wednesday 1/18/12 - Connectivity. Speaker: Jesse Brown==

OUTLINE Required Readings

• READING
• Slides from Dr. Lee's presentation (pending)

Suggested Further Reading

• Hageman DTI Slides
• Hageman DTI Notes 2/26/12
• Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69

Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):

• Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19
• Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39

Week 4 Applied fMRI, Diffusion Tractography

There is enormous subtlety to the design of pyschophysical and psychological studies made more complex by fitting the experiments into the constrained environment of the MR instrument, the limitations of the BOLD signal and the practical problems of time. This week, Dr. Bookheimer will introduce the design of human functional imaging experiments from the point of view of exposing cognitive process using fMRI.

Friday 1/24/12 - Experimental Design. Speaker: Susan Bookheimer

OUTLINE Required Readings

• Experimental Design lecture slides (2011)

Suggested Further Reading

• Russ Poldrack experimental design lecture (part 1)
• Russ Poldrack experimental design lecture (part 2)
• Experimental design lecture
• Experimental Design lecture slides (2010)

Wednesday 1/26/12 - Tractography using MRI Diffusion. Speaker: Nathan Hageman

File:DSIClusteringTwo.jpg

OUTLINE Required Readings

Week 5 MEG, EEG, Low Field MRI

Dr. Simpson is a leading expert in the use of scalp electrophysiology (EEG and MEG) to explore the dynamical processes of the human brain, and the integration of activity across cortex in complex human behaviors. Notably, the MEG instrument also uses the SQUID technology

Konstantin Penanen, together with Inseob Hahn and Byeong Ho Eom, have created a highly unusual MR imaging instrument that collects data in a magnetic field less than that of the earth. The tool uses Superconductin QUantum Interference Devices (SQUIDs) that detect the magnetic resonance imaging signal by direct magnetometry, rather than by induction.

Friday 1/31/12 - MEG and EEG. Speaker: Greg Simpson

A story

Suggested Reading

J Neurosci. 2008 Aug 13;28(33):8268-72. "Very slow EEG fluctuations predict the dynamics of stimulus detection and oscillation amplitudes in humans". Monto S, Palva S, Voipio J, Palva JM.

Friday 2/2//12 - Ultralow field MRI. Speaker: Konstantin Penanen NASA/CalTech Jet Propulsion Laboratory

OUTLINE

File:MiniscanGB.jpg

• Penanen Lecture Slides

Suggested Further Reading

• Parallel MRI at microtesla fields. Zotev VS, Volegov PL, Matlashov AN, Espy MA, Mosher JC, Kraus RH Jr. J Magn Reson. 2008 Jun;192(2):197-208. Epub 2008 Mar 6

• Three-dimensional prepolarized magnetic resonance imaging using rapid acquisition with relaxation enhancement. Matter NI, Scott GC, Venook RD, Ungersma SE, Grafendorfer T, Macovski A, Conolly SM. Magn Reson Med. 2006 Nov;56(5):1085-95.

• How the SQUID was born. AH Silver. Superconductor Science and Technology Volume 19, Number 5, 2006

• John Clarke, SQUIDs: Scientific American, August 1994.

Week 6 PET and TMS

Positron Emission Tomography was the first tomographic means available to explore neural activity in humans. Though this use was made much less common with the advent of fMRI, PET has many tricks up its sleeve. In particular, the technology allows incomparable sensitivity in the localization specific molecular species.

Transcranial Magnetostimulation is fundamentally different than the other technologies we have explored, in that it is used specifically to alter ongoing brain activity. While not exactly an imaging method, the TMS instrument is image-guided and uses tomographic placement.

Friday 2/7/12 - Positron Emission Tomography (PET). Speaker: Magnus Dahlbom

OUTLINE

File:ParallaxError.jpg

Required Readings

• PET Imaging handout

Suggested Further Reading

• READING

Wednesday 2/9/12 - Transcranial Magneto Stimulation (TMS). Speaker: Allan Wu

'Required Readings

• Wu 2011 Lecture slides
• TMS Safety and Ethics - Rossi, 2009
• | M Sandrini, C Umilta and E Rusconi, “The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.” Neurosci Biobehav Rev, 35(3): p. 516-536. 2011

Suggested Further Reading

• Handout for Wu TMS Lecture, 2010

Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:

• MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990

Week 7 Spectroscopy and PET

Both PET and MRI are means of localizing specific molecular species. MRI has lower sensitivity but good quantitative accuracy and the ability to simultaneously image and study multiple molecules and compounds. Our lecture on PET will consider the actual imaging device, its sensitivity and its limitations.

Friday 2/14/12 - Magnetic Resonance Spectroscopy. Speaker: Jeffry Alger

OUTLINE Required Readings

• Spectroscopy Lecture Slides

Suggested Further Reading A question came up from the audience about the problem of simultaneously space and chemical shift by frequency. For an amusing story about the problem, you might want to read:

• MS Cohen and D Baird, “Why Trade?: How zones of trade support epistemic stability.” Perspective on Science, 7(2): p. 231-254. 1999.

Wednesday 2/16/12- Positron Emission Tomography (PET) Applications. Speaker: Edythe London

OUTLINE

File:SmokerStroop.png

Required Readings

• PET Applications handout
• “Mapping human brain monoamine oxidase A and B with ¹¹C-labeled suicide inactivators and PET.” Science, 235(4787): p. 481-485. 1987.
• Mukherjee: Radiopharmaceuticals for Brain Imaging
• Imaging Neurotransmitter Release by Drugs of Abuse, Diana Martinez and Rajesh Narendran

Suggested Further Reading

• n/a

Week 8 Machine Learning

This week we will look at modern and advanced analytic methods broadly called machine learning, or statistical pattern analysis. These methods are of great interest in the imaging community as they offer high sensitivity, the ability to explore activity at the systems level and the potential for predictive analysis and brain reading.

Friday 2/21/12 - Presidents Day.

Suggested Further Reading

• George Washington
• Abraham Lincoln

Wednesday 2/23/12 - PCA, ICA, Machine learning. Speaker: Alan Yuille

OUTLINE

File:Probmodel.jpg

Required Readings

• READING

Suggested Further Reading

• READING

Week 9 Functional Connectivity, Multimodal Integration

WEEKLYSUMMARY

Friday 2/28/12 - Functional Connectivity. Speaker: Agatha Lenartowicz

OUTLINE

Required Readings

• Functional Connectivity Lecture Slides

Suggested Further Reading

Useful software for exploring functional connectivity (correlations/bivariate/partial etc) from Susan Whitfield-Gabrieli at MIT (link courtesy of Sam):*[1]

And additional readings in defense of DCM (other key papers are referenced in the slides)

Lee et al 2006 "Large-scale neural models and dynamic causal modelling"

David et al 2008 "Identifying Neural Drivers with Functional MRI: An Electrophysiological Validation"

Schuyler et al 2010 "Dynamic Causal Modeling applied to fMRI data shows high reliability"

Wednesday 3/2/12 - Multimodal Integration. Speaker: Cohen

OUTLINE Required Readings

• Lecture Slides for 3-2-11

Week 10 tbd

This week is presently left open for added topics and makeup as needed.

Friday 3/7/12 - Final Distributed. MSC

OUTLINE Required Readings

• READING

Suggested Further Reading

• READING

Wednesday 3/9/12 - Paul Weiss and Anne Andrews: Cohen

Direct Nanoscale and Molecular Imaging. Required Readings

• Andrews Lecture Slides
• Weiss Lecture Slides

Suggested Further Reading

• READING