Principles of Neuroimaging B - 2015

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Principles of Neuroimaging B, Winter, 2015 - Class Schedule and Syllabus

Main course page for Principles of Neuroimaging (2014-15)
M284A Principles of Neuroimaging A

Week 1 - MRI and fMRI

Monday 1/5/15

- MRI II Speaker: 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

OUTLINE Required Readings

HahnFig1.png above: Figure 1 from Hahn, 1950

Suggested Further Reading

Wednesday 1/7/15

- fMRI and MotionSpeaker: Cohen

Week 2 - Artifacts, Image Quality, Diffusion

Monday 1/1215

- Artifacts Speaker: Cohen

Wednesday 1/14/15

- 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):

Week 3 - Holiday and a canceled class

Monday 1/19/15

Martin Luther King Day

Wednesday 1/21/15

Class canceled due to other academic commitments. Sorry

Week 4 - Optics, SQUIDs MRI Contrast

Monday 1/26/15

Optics I. Speaker: Zachary Taylor

The overall goal of this lecture is to establish that: - Physical constants have tangible meanings - Plane waves form a physically unrealizable but extremely good approximation to real systems - Boundaries bend light - Physical constants, plane wave mechanics, and boundaries can be used to describe the operation of a lens - The PSF gives a good indication of the overall performance of an imaging system - All of these concepts have analogues in other areas of engineering (ie circuits, mechanical vibrations, etc.)''


  • Constitutive parameters (ε, μ, η, n, etc.)
  • Plane wave basics
  • Plane waves at boundaries
  • Lenses
  • Advanced imaging properties of lenses
  • Point spread function.

Required Readings Zach has very kindly agreed to post his Optics lecture notes. Suggested Further Reading

Wednesday 1/28/15

SQUIDs and MRI Contrast Agents. Speaker: Massoud Akhtari

Superconducting QUantum Interference Devices

  • What is superconductivity
  • What are SQUIDs
  • Basic physics of SQUIDs
  • Basic principles of measuring small magnetic fields
  • Applications

Suggested Further Readings

Principles and roles of contrast agents on MRI

  • What are contrast agents
  • What are the physical principles of MRI contrast agents
  • Different classes of MRI contrast agents: Passive vs active
  • examples of various contrast agents
  • Physiological and safety requirements of contrast agents
  • Targeted contrast agents

Suggested Further Readings

Week 5. Optics and New Optical Methods

Monday 2/2/15

- Optics II. Speaker: Zachary Taylor

Required Readings

  • Continued from prior week

Wednesday 2/4/15 - Trans-blood and TeraHertz Imaging Speaker: Warren Grundfest

Required Readings

Optional Readings

Week 6 Ultrasound and Optogenetics

Monday 2/9/15

Ultrasound. Speaker: George Saddik

Required Readings

Wednesday 2/11/15

Optogenetics. Speaker: Tom Otis

Required Readings

Week 7 PET

Monday 2/16/15

President's Day Vacation - No Class

Wednesday 2/18/15

Positron Emission Tomography. Speaker: Magnus Dahlboun

Handouts distributed in class.

Week 8 PET and Spectroscopy

Monday 2/23/15

PET applications. Speaker: Edythe London

Wednesday 2/25/15

- Spectroscopy Speaker: Joe O'Neill

Required Readings

Week 9 Transcranial Magnetostimulation and Brain Stimulation

Monday 3/2/15

Class canceled due to scheduling problems.

Wednesday 3/4/15

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:


Week 10

Monday 3/9/15

- Multimodal imaging. Speaker: Mark Cohen -

Required Readings

Wednesday 3/11/15

- Brain Stimulation. Speaker: Alexander Bystritsky

Required Readings