Principles of Neuroimaging B - 2017: Difference between revisions

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Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus
Principles of Neuroimaging B, Winter, 2017 - Class Schedule and Syllabus


== This schedule ''will'' change!==
== This schedule is a draft only and ''will'' change!==


:'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''
:'''[[Principles_of_Neuroimaging_-_2016-2017 | 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=
=Course Reading=
Line 22: Line 19:
:'''NOTE:'''  if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.
:'''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=
=Week 1: Magnetic Resonance Imaging: Fundamentals=
==''Monday 1/4/16'' ==
 
===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen 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
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''
''Required Readings''
:*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]
:*[[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.
:*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.
''Suggested Further Reading''
:*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource
:*[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'']
:*[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''
[[image:PSatSeq.jpg|right]]
''Required Readings''
:*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]


[[Image:HahnFig1.png | center]]}
==''Monday 1/9/17'' ==
<div style="text-align: center;">Figure 1 from Hahn, 1950</div>
===- MR Physics I. ''Speaker'': [https://www.brainmapping.org/MarkCohen/aboutmark.html Mark Cohen]===


==''Wednesday 1/6/16'' ==
==''Wednesday 1/11/17'' ==
===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
===- MR Physics II. ''Speaker'': [https://www.brainmapping.org/MarkCohen/aboutmark.html Mark Cohen]===




=Week 2: MRI Techniques=
=Week 2: MRI Techniques=
==''Monday 1/11/16'' ==
==''Monday 1/16/17'' ==
[[Image:ASL.png | right]]
===MLK Day No Class===
===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===
 
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.
==''Wednesday 1/18/17'' ==
===- MR Spatial Encoding Q&A. ''Speaker'' Cameron Rodriguez===
 
 
=Week 3: MRI Applications =
==''Monday 1/23/17'' ==
===- MR Pulse Sequences and Parameters ''Speaker'' [https://www.brainmapping.org/MarkCohen/aboutmark.html Mark Cohen]===
 
==''Wednesday 1/25/17'' ==
===- MR Applications (MR, fMRI, DTI, ASL, Spectroscopy). ''Speaker'' [https://www.brainmapping.org/MarkCohen/aboutmark.html Mark Cohen]===


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.
=Week 4: Multimodal Imaging=
==''Monday 1/30/17 CLASS IN SEMEL 67-415''==
===- Multimodal I ''Speaker'' Cameron Rodriguez===


''Required Readings'' - Please complete these readings prior to class.
==''Wednesday 2/1/17'' ==
:*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]
===- Multimodal II ''Speaker'' Agatha Lenartowicz===
<!--
:*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]
:*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]
[[Image:HahnFig1.png]]
''above'': Figure 1 from Hahn, 1950
-->
''Suggested Further Reading''
:*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]
:*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]
:*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]
:*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]
:*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]


==''Wednesday 1/13/16'' ==
:*[[media:eegfmritalk.pdf‎ | Lecture Slides]]
===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
:*[[media:chapter7.pdf‎ | EEG Instrumentation]]
:*[[media:chapter8.pdf‎ | EEG Quality I]]
:*[[media:chapter9.pdf‎ | EEG Quality II]]
:*[[media:chapter10.pdf‎ | Image Quality]]


''Required Readings'' - Please complete these readings prior to class.
=Week 5: Review =
<!--
==''Monday 2/6/17''==
:*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]
===- Q&A Class ===
:*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]
[[Image:HahnFig1.png]]
''above'': Figure 1 from Hahn, 1950
-->


''Suggested Further Reading''
==''Wednesday 2/8/17''==
===- Midterm Review===


=Week 3: tbd=
=MIDTERM=
==''Monday 1/18/16'' ==
===- MLK School Holiday===


==''Wednesday 1/20/16'' ==
===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
Abstract


''Required Readings'' - Please complete these readings prior to class.
=Week 6: Image Processing=
:*
==''Monday 2/13/17'' ==
<!--
===cont. Midterm Review===
:*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]
:*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]
[[Image:HahnFig1.png]]
''above'': Figure 1 from Hahn, 1950
-->
''Suggested Further Reading''
:*


=Week 4: Multimodal imaging=
==''Wednesday 2/15/17'' ==
==''Monday 1/25/16'' ==
===-Image Processing I. ''Speaker'' Cameron Rodriguez===
===Multimodal imaging. ''Speaker'':  [http://www.brainmapping.org/MarkCohen MarkCohen]===
Handouts distributed in class.


''Required Readings'' - Please complete these readings prior to class.
=Week 7: Image Analysis=
:*[[media:MultimodalNITP.pdf | slides handout]]
==''Monday 2/20/17'' ==
===President’s Day Holiday No Class===


<!--
==''Wednesday 2/22/17'' ==
:*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]
===- Image Processing II. ''Speaker'' Agatha Lenartowicz===
:*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]
[[Image:HahnFig1.png]]
''above'': Figure 1 from Hahn, 1950
-->
''Suggested Further Reading''
:*


==''Wednesday 1/27/16'' ==
=Week 8: Image Analysis Cont.=
===Class canceled.===
==''Monday 2/27/17 CLASS IN SEMEL 67-415'' ==
===Analysis I ''Speaker'' Agatha Lenartowicz===


=Week 5: Positron Emission Tomography=
==''Wednesday 3/1/17'' ==
[[Image:PET-ring.png | left]]
===- Analysis II ''Speaker'' Agatha Lenartowicz===
==''Monday 2/1/16'' ==
===Positron Emission Tomography. ''Speaker'':  [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===
Handouts distributed in class.


''Required Readings'' - Please complete these readings prior to class.
=Week 9: Brain Decoding=
:*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]
==''Monday 3/6/17'' ==
===-ML I: Dimension Reduction, Machine Learning Fundamentals ''Speaker'' Wesley Kerr, Ph.D.===


<!--
==''Wednesday 3/8/17'' ==
:*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]
===- MLII: Machine Learning cont. ''Speaker'' Wesley Kerr, Ph.D.===
:*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]
[[Image:HahnFig1.png]]
''above'': Figure 1 from Hahn, 1950
-->
''Suggested Further Reading''
:*


[[Image:PETfounders.png | right]]
=Week 10: Review=
==''Monday 3/13/17'' ==
===-TBD ''Speaker'' TBD===


==''Wednesday 2/3/16'' ==
==''Wednesday 3/15/17'' ==
===PET applications. ''Speaker'':  [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===
===-Final Exam Review. ''Speaker'' TBD===
''Required Readings'' - Please complete these readings prior to class.
:*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] <-- '''Modified 2-3-16'''
''Suggested Further Reading''


=Week 6: Brain Stimulation and Ultrasound=
==''Monday 2/8/16'' ==
===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===


'Required Readings''
:* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''<- modified 2-9-2016'''
:* [[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]


''Suggested Further Reading''
Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:
:*[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 2/10/16'' ==
[[Image:Cetacean.png | right]]
===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===
''Required Readings''
:*[[media:US_Imaging_Systems_1.pdf | Ultrasound Slides (2016)]]


''Suggested Further Reading''
<!--
:* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]
[[Image:ASL.png | right]]
:*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]
===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===
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.


=Week 7: Optical neuroimaging and optogenetics=
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.
==''Monday 2/15/16'' ==
===- President's Day - School holiday: ===


==''Wednesday 2/17/16'' ==
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.
[[Image:PTEN.png | left]]
===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===


''Required Readings'' - Please complete these readings prior to class.
''Required Readings'' - Please complete these readings prior to class.
:*[[media:Golshani_NITP_2016.pdf | Dr. Golshani's Methods slides]]
:*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]
:*[[media:PeymanResearchTalk.pdf | Dr. Golshani's Research slides]]
 
:*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]
:*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]
[[Image:HahnFig1.png]]
''above'': Figure 1 from Hahn, 1950
 
''Suggested Further Reading''
''Suggested Further Reading''
:*
:*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]
:*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]
:*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]
:*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]
:*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]
 
 


=Week 8: Advanced MRI methods=
=Week 8: Advanced MRI methods=
Line 237: Line 205:
:*[[media:Flint_and_Geschwind.pdf | ''Genetics and genomics of psychiatric disease'' Flint and Geschwind]]
:*[[media:Flint_and_Geschwind.pdf | ''Genetics and genomics of psychiatric disease'' Flint and Geschwind]]


==''Wednesday 3/9/16'' ==
 
===- Course wrap up and review.  ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
-->

Latest revision as of 04:01, 9 February 2017

Principles of Neuroimaging B, Winter, 2017 - Class Schedule and Syllabus

This schedule is a draft only and will change!

Back to main course page for Principles of Neuroimaging

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: Fundamentals

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

Required Readings

Monday 1/9/17

- MR Physics I. Speaker: Mark Cohen

Wednesday 1/11/17

- MR Physics II. Speaker: Mark Cohen

Week 2: MRI Techniques

Monday 1/16/17

MLK Day No Class

Wednesday 1/18/17

- MR Spatial Encoding Q&A. Speaker Cameron Rodriguez

Week 3: MRI Applications

Monday 1/23/17

- MR Pulse Sequences and Parameters Speaker Mark Cohen

Wednesday 1/25/17

- MR Applications (MR, fMRI, DTI, ASL, Spectroscopy). Speaker Mark Cohen

Week 4: Multimodal Imaging

Monday 1/30/17 CLASS IN SEMEL 67-415

- Multimodal I Speaker Cameron Rodriguez

Wednesday 2/1/17

- Multimodal II Speaker Agatha Lenartowicz

Week 5: Review

Monday 2/6/17

- Q&A Class

Wednesday 2/8/17

- Midterm Review

MIDTERM

Week 6: Image Processing

Monday 2/13/17

cont. Midterm Review

Wednesday 2/15/17

-Image Processing I. Speaker Cameron Rodriguez

Week 7: Image Analysis

Monday 2/20/17

President’s Day Holiday No Class

Wednesday 2/22/17

- Image Processing II. Speaker Agatha Lenartowicz

Week 8: Image Analysis Cont.

Monday 2/27/17 CLASS IN SEMEL 67-415

Analysis I Speaker Agatha Lenartowicz

Wednesday 3/1/17

- Analysis II Speaker Agatha Lenartowicz

Week 9: Brain Decoding

Monday 3/6/17

-ML I: Dimension Reduction, Machine Learning Fundamentals Speaker Wesley Kerr, Ph.D.

Wednesday 3/8/17

- MLII: Machine Learning cont. Speaker Wesley Kerr, Ph.D.

Week 10: Review

Monday 3/13/17

-TBD Speaker TBD

Wednesday 3/15/17

-Final Exam Review. Speaker TBD

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