Principles of Neuroimaging B - 2016

Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus

This schedule will change!

Back to main course page for Principles of Neuroimaging

Lecture Videos

Hopefully, we can start recording the class sessions for those who cannot make a few lectures.

Course Reading

Required Reading

Signal Processing for Neuroscientists by Wim van Drongelen

This can be found as a PDF on scribd.com, for a small fee of $8.99

Supplemental Reading

Matlab for Neuroscientists

Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists

Cartoon Guide to Statistics

Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics

NOTE: if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.

Week 1: Magnetic Resonance Imaging

Monday 1/4/16

- MRI Contrast. Mark Cohen: Mark Cohen

Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible 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

Required Readings

• MRI Slides
• These notes by Joseph Hornak are highly professional and complete coverage of MRI.

Suggested Further Reading

• eMRI is another excellent online MRI learning resource
• Erwin Hahn - Spin Echoes: Essential reading for the MRI community

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Figure 1 from Hahn, 1950

Week 2: MRI Techniques

Monday 1/11/16

- Measurement of Blood Flow by MRI. Danny JJ Wang: [1]

Most MRI images in use today are static maps, generally called "structural" images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term "functional" to describe images that pick up time-varying signals. The term functional MRI, of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.

Measurement of blood flow in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.

In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.

Required Readings - Please complete these readings prior to class.

• Dr. Wang's Handout

Suggested Further Reading

• Williams, PNAS 1992
• Detre, MRM 1992
• Dai, MRM 2008
• Wu, MRM 2007
• Zheng, Neuroimage 2012

Wednesday 1/13/16

- More MRI. Mark Cohen: Mark Cohen

Required Readings - Please complete these readings prior to class.

Suggested Further Reading

Week 3: tbd

Wednesday 1/20/16

- tbd. Speaker: Mark Cohen

Abstract

Required Readings - Please complete these readings prior to class.

Suggested Further Reading

Week 4: Multimodal imaging

Monday 1/25/16

Multimodal imaging. Speaker: MarkCohen

Handouts distributed in class.

Required Readings - Please complete these readings prior to class.

• slides handout

Suggested Further Reading

Week 5: Positron Emission Tomography

Monday 2/1/16

Positron Emission Tomography. Speaker: Magnus Dahlboun

Handouts distributed in class.

Required Readings - Please complete these readings prior to class.

• Dr. Dahlbom's PET handout

Suggested Further Reading

Wednesday 2/3/16

PET applications. Speaker: Edythe London

Required Readings - Please complete these readings prior to class.

• Dr. Edythe London PET Slides <-- Modified 2-3-16

Suggested Further Reading

Week 6: Brain Stimulation and Ultrasound

Monday 2/8/16

TMS. Speaker: Allan Wu

'Required Readings

• Wu Lecture slides 2016 <- modified 2-9-2016
• 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 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

Wednesday 2/10/16

Ultrasound. Speaker: George Saddik

Required Readings

• Ultrasound Slides (2016)

Suggested Further Reading

• A review of tissue substitutes for ultrasound imaging
• Ultrasound Slides (2015)

Week 7: Optical neuroimaging and optogenetics

Wednesday 2/17/16

- Optical Neuroimaging and Optogenetics. Speaker: Peyman Golshani:

Required Readings - Please complete these readings prior to class.

• Dr. Golshani's Methods slides
• Dr. Golshani's Research slides

Suggested Further Reading

Week 8: Advanced MRI methods

Monday 2/22/16

- Diffusion Physics Speaker: Ben Ellingson

Required Readings Slides should be up soon.

• Handouts for class on 1/14/15 <- New 1/26-2015
• Ben Ellingson Diffusion Slides uploaded 3/14/14

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

Wednesday 2/25/16

- Brain Morphometry. Speaker: Roger Woods:

Required Readings - Please complete these readings prior to class.

• Dr. Woods' slides

Suggested Further Reading

*RP Woods, “Characterizing volume and surface deformations in an atlas framework: theory, applications, and implementation.” Neuroimage, 18(3): p. 769-788. 2003

Week 9: MR Spectroscopy

Monday 2/29/16

No class

Wednesday 3/2/16

Spectroscopy fundamentals. Speaker: Joseph O'Neill

Required Readings - Please complete these readings prior to class.

• Dr. O'Neill's slides

- Spectroscopic Methods. Speaker: Albert Thomas

Required Readings - Please complete these readings prior to class.

• Dr. Thomas' slides

Suggested Further Reading

• SA Wijtenburg, LM Rowland, RA Edden and PB Barker, “Reproducibility of brain spectroscopy at 7T using conventional localization and spectral editing techniques.” J Magn Reson Imaging, 38(2): p. 460-467. 2013. PMCID: PMC3620961
• S Lipnick, G Verma, S Ramadan, J Furuyama and MA Thomas, “Echo planar correlated spectroscopic imaging: implementation and pilot evaluation in human calf in vivo.” Magn Reson Med, 64(4): p. 947-956. 2010. PMCID: PMC2946523
• JK Furuyama, NE Wilson, BL Burns, R Nagarajan, DJ Margolis and MA Thomas, “Application of compressed sensing to multidimensional spectroscopic imaging in human prostate.” Magn Reson Med, 67(6): p. 1499-1505. 2012.

Week 10: Multimodal Methods / Course wrap up

Monday 3/7/16

- Imaging Genetics. Speaker: Carrie Bearden:

Required Readings - Please complete these readings prior to class.

• Dr. Bearden's slides

Suggested Further Reading

• Enhancing the Informativeness and Replicability of Imaging Genomics Studies Carter et al.
• Genetics and genomics of psychiatric disease Flint and Geschwind