Principles of Neuroimaging B - 2015: Difference between revisions

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


:'''[[Principles_of_Neuroimaging_-_2014-2015 | Main course page for Principles of Neuroimaging (2012-13)]]'''
:'''[[Principles_of_Neuroimaging_-_2014-15 | Main course page for Principles of Neuroimaging (2014-15)]]'''


:'''[[Principles_of_Neuroimaging_A_-_2014 | M284A Principles of Neuroimaging A]]'''
:'''[[Principles_of_Neuroimaging_A_-_2014 | M284A Principles of Neuroimaging A]]'''
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==''Monday 1/5/15''==
==''Monday 1/5/15''==
===- MRI II ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]===
===- MRI II ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]===
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
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
OUTLINE
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=Week 2 - Artifacts, Image Quality, Diffusion=
=Week 2 - Artifacts, Image Quality, Diffusion=
==''Monday 1/1215'' ==
==''Monday 1/1215'' ==
===- Artifacts ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]===
=== - Artifacts ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]===


==''Wednesday 1/14/15==
==''Wednesday 1/14/15''==
===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&action=detail&ref=18 Ben Ellingson]===
===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&action=detail&ref=18 Ben Ellingson]===
''Required Readings''
''Required Readings''
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:*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]
:*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]


=Week 3 - Swine flu and MRI=
=Week 3 - Holiday and a canceled class=
==''Monday 1/20/15''==
==''Monday 1/19/15''==
===Class canceled due to flu. Sorry===
===Martin Luther King Day===
==''Wednesday 1/22/15''==
:*[http://www.imdb.com/title/tt1020072/ Selma - a great choice]
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


OUTLINE
==''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'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]===
[[Image:Reflection.jpg|right]]
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.)''''
 
'''Outline:'''
:* 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 [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].
''Suggested Further Reading''
 
==''Wednesday 1/28/15''==
===SQUIDs and MRI Contrast Agents. ''Speaker'': [https://people.healthsciences.ucla.edu/institution/personnel?personnel_id=75147 Massoud Akhtari]===
 
=Week 5. Optics and New Optical Methods=
==''Monday 2/2/15''
=== - Optics II. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]===
''Required Readings''
''Required Readings''
:*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]
:* Continued from prior week
:*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.
:*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource
:*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']
[[Image:HahnFig1.png]]
''above'': Figure 1 from Hahn, 1950


''Suggested Further Reading''
==''Wednesday 2/4/15'' - Trans-blood and TeraHertz Imaging ''Speaker'': [http://www.bioeng.ucla.edu/people/faculty/Faculty/warren-s.-grundfest-m.d Warren Grundfest]==
[[image:PSatSeq.jpg|right]]
''Required Readings''
=Week 4 - Magnetic Resonance Imaging=
:*


==''Monday 1/27/1'' - MRI==
=Week 6 Ultrasound and Optogenetics=
===-MRI I ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]===
==''Monday 2/9/15''==
===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===
''Required Readings''
:*
==''Wednesday 2/11/15''==
===Optogenetics. ''Speaker'': [http://www.otislab.org/people.html Tom Otis]===
''Required Readings''
''Required Readings''
:*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]
:*
==''Wednesday 1/29/15'' - MRI II. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]==


=Week 5 MRI and multimodal imaging=
=Week 7 PET=
==''Monday 2/3/15''==
==''Monday 2/16/15''==
===MRI (fMRI) III. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]===
===President's Day Vacation - No Class===
==''Wednesday 2/5/15''==
===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]===
:* [[Media:MultiModalNITP2013-sm.pdf | Multimodal neuroimaging lecture slides]]


=Week 6 Diffusion and PET=
==''Wednesday 2/18/15''==
==''Monday 2/10/15''==
===Diffusion imaging.
==''Wednesday 2/12/15''==
===Positron Emission Tomography. ''Speaker'':  [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===
===Positron Emission Tomography. ''Speaker'':  [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===
Handouts distributed in class.
Handouts distributed in class.


=Week 7=
=Week 8 PET and Spectroscopy=
==''Monday 2/17/15'' Presidents Day - No class==
==''Monday 2/23/15''==
==''Wednesday 2/19/15''==
===PET applications. ''Speaker'':  [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===
 
:*[[Media:London_NITP_PET_2-26-14_sm.pdf | Dr. Edythe London PET Slides]]
 
==''Wednesday 2/25/15''==
=== - Spectroscopy  ''Speaker'':  [https://people.healthsciences.ucla.edu/research/institution/personnel?personnel_id=74852 Joe O'Neill]===
''Required Readings''
:*


=Week 8 Transcranial Magnetostimulation and PET applications=
=Week 9 Transcranial Magnetostimulation and Brain Stimulation=
==''Monday 2/24/15''==
==''Monday 3/2/15''==
===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===
===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===
'Required Readings''
'Required Readings''
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:*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf 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]
:*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf 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 2/26/1.==
==''Wednesday 3/4/15''==
===PET applications. ''Speaker'':  [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===
===PET applications. ''Speaker'':  [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===


:*[[Media:London_NITP_PET_2-26-14_sm.pdf | Dr. Edythe London PET Slides]]
=Week 10=
==''Monday 3/9/15''==
''Required Readings''
:*
 
==''Wednesday 3/11/15''==
''Required Readings''
:*
 


=Week 9 - Spectroscopy=
==''Monday 3/3/15'' - Class canceled==
==''Wednesday 3/5/15''==
===Spectroscopy. ''Speaker:'' [http://radiology.ucla.edu/body.cfm?id=48&action=detail&ref=65 Albert Thomas]===
===Spectroscopy. ''Speaker:'' [http://radiology.ucla.edu/body.cfm?id=48&action=detail&ref=65 Albert Thomas]===
Handouts distributed in class
Handouts distributed in class

Revision as of 05:27, 24 January 2015

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

File:PSatSeq.jpg

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

File:Reflection.jpg

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.)''

Outline:

  • 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

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

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

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 3/4/15

PET applications. Speaker: Edythe London

Week 10

Monday 3/9/15

Required Readings

Wednesday 3/11/15

Required Readings


Spectroscopy. Speaker: Albert Thomas

Handouts distributed in class

Week 10 - Compressed sensing and finals

Monday 3/10/15

Compressed Sensing. Speaker: Ming Yan

To access the slides from the course web site listed on his handout, The username is "caame654", and password is "dense".

Suggested Further Reading

  • READING
"An Introduction to Compressive Sampling" EJ Candes, MB Watkin, IEEE Signal Processing Magazine, March, 2008 <-- Mark's favorite. This is a good overview of the field.
"Sparse MRI: The Application of Compressed Sensing for Rapid MR Imaging" M. Lustig, D. Donoho, J.M. Pauly, Magn. Reson. Med 58:1182–1195, 2007 Lustig demonstrates each step in the process with examples using MRI.
"Compressed Sensing", D. Donoho, IEEE Trans. Inform. Theory 52:1289, 2006 One of the more accessible formal discussions of CS
Rice University Compressed Sensing Resources. A repository of scholarly work on CS.
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