Principles of Neuroimaging B - 2012

Principles of Neuroimaging B, Winter, 2012 - 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 1/11/12 - 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

File:PSatSeq.jpg

Friday 1/13/12 - 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 1/18/12 - Connectivity. Speaker: Jesse Brown

OUTLINE Required Readings

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

Suggested Further Reading

• READING

Week 3 Advanced MRI Applications and TMS

Wednesday 1/25/12 - Diffusion. Speaker: Jeffry Alger

OUTLINE

File:Bandwidth.jpg

Required Readings

• DTI lecture notes
• Spectroscopy lecture notes.

'Suggested Readings

• DTI basics and future directions

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

• 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 4 PET

Wednesday 2/1/12 - Positron Emission Tomography (PET). Speaker: Magnus Dahlbom

OUTLINE

File:ParallaxError.jpg

Required Readings

• PET Imaging handout

Suggested Further Reading

• READING

Friday 2/3/12- 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 5 fMRI and Ultrasound

Wednesday 2/8/12 - Multimodal imaging. Speaker: Cohen

OUTLINE Required Readings

• Multimodal imaging handout

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

]

• Brain operations guided by real-time two-dimensional ultrasound: new possibilities as a result of improved image quality.” Neurosurgery, 51(2): p. 402-411; discussion 411-402. 2002
• Biomed 298 Design of Medical Ultrasound

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

• Review of connectivity

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

Brain Stimulation

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

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 - Compressive Sensing. Kevin Kelly - Rice University

OUTLINE Compressed sensing lecture by Dr. Kevin Kelly of Rice University.

Required Readings

• Compressed imaging handout

Suggested Further Reading

• READING

Week 10

Wednesday 3/14/12 - Single-Molecule Biological Structure: Microwave Scanning Tunneling Microscopy of Peptides. Shelley Claridge

OUTLINE Required Readings

• Single molecule imaging

Suggested Further Reading

• READING

Friday 3/16/12 - Machine Learning. Alan Yuille

OUTLINE Required Readings

Suggested Further Reading

• READING

FINALS

3/19-23/12