Principles of Neuroimaging B - 2016

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

Contents

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

Suggested Further Reading

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Figure 1 from Hahn, 1950

Wednesday 1/6/16

- MRI Image Formation and fMRI. Mark Cohen: Mark Cohen

Week 2: MRI Techniques

Monday 1/11/16

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- 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.

Suggested Further Reading

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

Monday 1/18/16

- MLK School Holiday

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.

Suggested Further Reading

Wednesday 1/27/16

Class canceled.

Week 5: Positron Emission Tomography

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Monday 2/1/16

Positron Emission Tomography. Speaker: Magnus Dahlboun

Handouts distributed in class.

Required Readings - Please complete these readings prior to class.

Suggested Further Reading

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Wednesday 2/3/16

PET applications. Speaker: Edythe London

Required Readings - Please complete these readings prior to class.

Suggested Further Reading

Week 6: Brain Stimulation and Ultrasound

Monday 2/8/16

TMS. Speaker: Allan Wu

'Required Readings

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

Wednesday 2/10/16

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Ultrasound. Speaker: George Saddik

Required Readings

Suggested Further Reading

Week 7: Optical neuroimaging and optogenetics

Monday 2/15/16

- President's Day - School holiday:

Wednesday 2/17/16

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- Optical Neuroimaging and Optogenetics. Speaker: Peyman Golshani:

Required Readings - Please complete these readings prior to class.

Suggested Further Reading

Week 8: Advanced MRI methods

Monday 2/22/16

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- Diffusion Physics Speaker: Ben Ellingson

Required Readings Slides should be up soon.

Suggested Further Reading

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

Wednesday 2/25/16

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- Brain Morphometry. Speaker: Roger Woods:

Required Readings - Please complete these readings prior to class.

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.

- Spectroscopic Methods. Speaker: Albert Thomas

Required Readings - Please complete these readings prior to class.

Suggested Further Reading

Week 10: Multimodal Methods / Course wrap up

Monday 3/7/16

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- Imaging Genetics. Speaker: Carrie Bearden:

Required Readings - Please complete these readings prior to class.

Suggested Further Reading

Wednesday 3/9/16

- Course wrap up and review. Mark Cohen: Mark Cohen