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''
Slides should be up soon.
Slides should be up soon.
:*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''<- New 1/26-2015''
:*[[media:1_DiffusionMRI_Methods_v1.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14
:*[[media:1_DiffusionMRI_Methods_v1.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14
''Suggested Further Reading''
''Suggested Further Reading''
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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]===
:* Lecture Slides:[[media:SQUIDs_Slides.pdf | SQUIDs Lecture Slides]]
''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''
:*[[media:W5 Baillet et al (2001).pdf | SQUIDs additional reading]]
 
''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''
:*[[media:MNP_physchem.pdf | MMP readings]]
 
=Week 5. Optics and New Optical Methods=
==''Monday 2/2/15''==
=== - Optics II. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]===
''Required Readings''
:* Continued from prior week
 
==''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]==
''Required Readings''
''Required Readings''
:*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]
:*
:*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.
''Optional Readings''
:*[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''
=Week 6 Ultrasound and Optogenetics=
[[image:PSatSeq.jpg|right]]
==''Monday 2/9/15''==
=Week 4 - Magnetic Resonance Imaging=
===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===
''Required Readings''
:*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides]]


==''Monday 1/27/1'' - MRI==
==''Wednesday 2/11/15''==
===-MRI I ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]===
===Optogenetics. ''Speaker'': [http://www.otislab.org/people.html Tom Otis]===
''Required Readings''
''Required Readings''
:*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]
:*[[media:Otis_optogenetics_lecture_2_11_15_SM.pdf | Optogenetics 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.
:*[[media:PET_2015_SM.pdf | Dr. Dahlbom's PET handout]]
=Week 8 PET and Spectroscopy=
==''Monday 2/23/15''==
===PET applications. ''Speaker'':  [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===


=Week 7=
:*[[Media:NITP_PET_2-23-15_SM.pdf | Dr. Edythe London PET Slides]]
==''Monday 2/17/15'' Presidents Day - No class==
==''Wednesday 2/19/15''==


=Week 8 Transcranial Magnetostimulation and PET applications=
==''Wednesday 2/25/15''==
==''Monday 2/24/15''==
=== - Spectroscopy  ''Speaker'':  [https://people.healthsciences.ucla.edu/research/institution/personnel?personnel_id=74852 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'': [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''
:* [[media:Wu-TMS-2014-02-24-sm.pdf | Wu Lecture slides]]
:* [[media:NITP-talk-2015-03-04-distribution_SM.pdf | Wu Lecture slides 2015]]
:* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]
:* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]
:* [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T0J-50CV801-1&_user=4423&_coverDate=01%2F31%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000059605&_version=1&_urlVersion=0&_userid=4423&md5=f9fa3c7d63942dfb3c74e047a1f848bc&searchtype=a | 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]
:* [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T0J-50CV801-1&_user=4423&_coverDate=01%2F31%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000059605&_version=1&_urlVersion=0&_userid=4423&md5=f9fa3c7d63942dfb3c74e047a1f848bc&searchtype=a | 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]
Line 100: Line 158:
:*[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.==
===tbd===
===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===
 
=Week 10=
==''Monday 3/9/15''==
=== - Multimodal imaging. ''Speaker:'' Mark Cohen - ===
''Required Readings''
:* [[media:MultiModalNITP2014_SM.pdf | Cohen Lecture slides 2014]]


:*[[Media:London_NITP_PET_2-26-14_sm.pdf | Dr. Edythe London PET Slides]]
==''Wednesday 3/11/15''==
=== - Brain Stimulation. ''Speaker:'' [http://www.uclahealth.org/body.cfm?xyzpdqabc=0&id=479&action=detail&ref=9872 Alexander Bystritsky] ===
''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
Line 124: Line 188:
::[http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=1614066 ''"Compressed Sensing"'', D. Donoho, IEEE Trans. Inform. Theory 52:1289, 2006] One of the more accessible formal discussions of CS
::[http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=1614066 ''"Compressed Sensing"'', D. Donoho, IEEE Trans. Inform. Theory 52:1289, 2006] One of the more accessible formal discussions of CS
::[http://dsp.rice.edu/cs Rice University Compressed Sensing Resources]. A repository of scholarly work on CS.
::[http://dsp.rice.edu/cs Rice University Compressed Sensing Resources]. A repository of scholarly work on CS.
-->

Latest revision as of 16:36, 19 March 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

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:

tbd

Week 10

Monday 3/9/15

- Multimodal imaging. Speaker: Mark Cohen -

Required Readings

Wednesday 3/11/15

- Brain Stimulation. Speaker: Alexander Bystritsky

Required Readings


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