Principles of Neuroimaging B - 2012: Difference between revisions
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Revision as of 17:33, 28 February 2012
Principles of Neuroimaging B, Winter, 2012 - Class Schedule and Syllabus
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 1/11/12 - 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
Friday 1/13/12 - MRI II. Speaker: Cohen
OUTLINE Required Readings
Suggested Further Reading
- READING
WEEKLY SUMMARY
Week 2 MRI Applications
Wednesday 1/18/12 - Connectivity. Speaker: Jesse Brown
OUTLINE Required Readings
Suggested Further Reading
- Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):
Suggested Further Reading
- READING
Friday 1/20/12 - Advanced MRI Pulse Sequences. Speaker: Daniel Ennis
Week 3 Advanced MRI Applications and TMS
Wednesday 1/25/12 - Diffusion. Speaker: Jeffry Alger
OUTLINE
Required Readings
Friday 1/27/12 - TMS (tentative). Speakers: Allan Wu,
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.
'Required Readings
Suggested Further Reading
Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:
Week 4 PET
Wednesday 2/1/12 - Positron Emission Tomography (PET). Speaker: Magnus Dahlbom
OUTLINE
Required Readings
Suggested Further Reading
- READING
Friday 2/3/12- Positron Emission Tomography (PET) Applications. Speaker: Edythe London
OUTLINE
Required Readings
Suggested Further Reading
- n/a
Week 5 fMRI and Ultrasound
Wednesday 2/8/12 - Multimodal imaging. Speaker: Cohen
OUTLINE Required Readings
Friday 2/10/12 - Ultrasound (tentative). Speaker: Martin Culjat
OUTLINE
Ultrasound is one of the earliest means of seeing into the body. Until recently, however, seeing into the brain has been very poor. Recent advances are improving on this.
Required Readings
Suggested Further Reading
- [http://www.jultrasoundmed.org/content/24/12/1671.full.pdf+html “Intraoperative sonography for neurosurgery.” J Ultrasound Med, 24(12): p. 1671-1682. 2005
]
Week 6
Wednesday 2/15/12 - Connectivity. "Jesse Brown"
OUTLINE
Connectivity in neuroimaging is a broad subject. These slides focus on resting state fMRI and DTI based connectivity methods and results.
Media:nitp_connectivity_02142012.pdf
Required Readings
Suggested Further Reading
- Networks of the Brain by Olaf Sporns
Links of interest
- INDI: the International Neuroimaging Data-sharing Initiative. A very useful source of publicly available fMRI and DTI data.
- Human Connectome Project: The WashU-UMinn consortium will scan 1200 individuals with resting state fMRI, DSI, and structural MRI, along with MEG and 7-Tesla scanning in some cases.
- UMCD: The UCLA Multimodal Connectivity Database, a web-based repository for brain network analysis and data sharing.
Friday 2/17/12 - Brain Stimulation. "Alexander Bystritsky"
OUTLINE Required Readings
Suggested Further Reading
- READING
Week 7
Wednesday 2/22/12 - Methods of Dimension Reduction. "Ariana Anderson"
OUTLINE Required Readings
Suggested Further Reading
- READING
Friday 2/25/12 - Bayesian Statistics. "Donatello Telesca"
OUTLINE Required Readings
Suggested Further Reading
- READING
Week 8
Wednesday 2/29/12 - CLASS IS CANCELLED FOR TODAY. SORRY
Friday 3/2/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Week 9
Wednesday 3/7/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Friday 3/9/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Week 10
Wednesday 3/14/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Friday 3/16/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
FINALS
3/19-23/12
==Friday 1//12 - fMRI. Speaker:
Cohen==
OUTLINE
Required Readings
Suggested Further Reading
- READING
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
Suggested Reading
Friday 2/2//12 - Ultralow field MRI. Speaker: Konstantin Penanen NASA/CalTech Jet Propulsion Laboratory
OUTLINE
Suggested Further Reading
- John Clarke, SQUIDs: Scientific American, August 1994.
Friday 2/7/12 - Positron Emission Tomography (PET). Speaker: Magnus Dahlbom
OUTLINE
Required Readings
Suggested Further Reading
- READING
Wednesday 2/9/12 - Transcranial Magneto Stimulation (TMS). Speaker: Allan Wu
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
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:
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
Wednesday 2/23/12 - PCA, ICA, Machine learning. Speaker: Alan Yuille
OUTLINE
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
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
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
Suggested Further Reading
- READING