Principles of Neuroimaging B - 2017: Difference between revisions

From Center for Cognitive Neuroscience
Jump to navigation Jump to search
(Created page with "Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus == This schedule ''will'' change!== :'''Principles_of_Neuroimaging_-_2015-2016 | Back to main cour...")
 
No edit summary
Line 1: Line 1:
Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus
Principles of Neuroimaging B, Winter, 2016 - 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 23: Line 20:


=Week 1: Magnetic Resonance Imaging=
=Week 1: Magnetic Resonance Imaging=
==''Monday 1/4/16'' ==
==''Monday 1/9/17’’ ==
===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
===- Pulse Sequences. ‘’Speaker’’: TBD===
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''
:*[[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.
''Suggested Further Reading''
:*[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 | center]]}
<div style="text-align: center;">Figure 1 from Hahn, 1950</div>
 
==''Wednesday 1/6/16'' ==
===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===


==''Wednesday 1/11/17’’ ==
===- MR Parameters. ‘’Speaker’’: TBD===


=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.


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.
==''Wednesday 1/18/17’’ ==
===-MR Applications (MR, fMRI, DTI, ASL, Spectroscopy). ‘’Speaker’’ TBD===


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 3: Non-MR Imaging=
==''Monday 1/23/17’’ ==
===- PET I. ‘’Speaker’’ TBD===


''Required Readings'' - Please complete these readings prior to class.
==''Wednesday 1/25/17’’ ==
:*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]
===- PET II. ‘’Speaker’’ TBD===
<!--
:*[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'' ==
[[Image:PET-ring.png | left]]
===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
[[Image:PETfounders.png | right]]


''Required Readings'' - Please complete these readings prior to class.
=Week 4: Non-MR Imaging=
<!--
==''Monday 1/30/17’’ ==
:*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]
===- Optogenetics I. ‘’Speaker’’ TBD===
:*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]
[[Image:HahnFig1.png]]
''above'': Figure 1 from Hahn, 1950
-->
 
''Suggested Further Reading''
 
=Week 3: tbd=
==''Monday 1/18/16'' ==
===- MLK School Holiday===


==''Wednesday 1/20/16'' ==
==''Wednesday 2/1/17’’ ==
===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
===- Optogenetics II. ‘’Speaker’’ TBD===
Abstract


''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: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''
:*
:*


=Week 4: Multimodal imaging=
=Week 5: Multimodal Imaging & Neuroimaging Data=
==''Monday 1/25/16'' ==
==''Monday 2/6/17’’ ==
===Multimodal imaging. ''Speaker'':  [http://www.brainmapping.org/MarkCohen MarkCohen]===
===- Multimodal Imaging ‘’Speaker’’ TBD===
Handouts distributed in class.


''Required Readings'' - Please complete these readings prior to class.
==''Wednesday 2/8/17’’ ==
:*[[media:MultimodalNITP.pdf | slides handout]]
===- Neuroimaging Data: Fundamentals. ‘’Speaker’’ TBD===
 
=MIDTERM=


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


==''Wednesday 1/27/16'' ==
==‘’Wednesday 2/15/17’’ ==
===Class canceled.===
===-Multivariate Analyses: Dimension Reduction. ‘’Speaker’’ TBD===


=Week 5: Positron Emission Tomography=
=Week 7: Neuroimaging Data=
[[Image:PET-ring.png | left]]
==''Monday 2/20/17’’ ==
==''Monday 2/1/16'' ==
===President’s Day Holiday No Class===
===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.
==''Wednesday 2/22/17’’ ==
:*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]
===- Multivariate Analyses: Brain Decoding ‘’Speaker’’ TBD===


<!--
=Week 8: Practical Brain Decoding & Connectivity=
:*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]
==''Monday 2/27/17’’ ==
:*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]
===Building a BCI System===
[[Image:HahnFig1.png]]
''above'': Figure 1 from Hahn, 1950
-->
''Suggested Further Reading''
:*


[[Image:PETfounders.png | right]]
==''Wednesday 3/1/17’’ ==
===- Connectivity Fundamentals ‘’Speaker’’ TBD===


==''Wednesday 2/3/16'' ==
=Week 9: Neuromodulation=
===PET applications. ''Speaker'':  [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===
==''Monday 3/6/17’’ ==
''Required Readings'' - Please complete these readings prior to class.
===-TMS. ‘’Speaker’’ TBD===
:*[[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=
==''Wednesday 3/8/17’’ ==
==''Monday 2/8/16'' ==
===- Ultrasound. ‘’Speaker’’ TBD===
===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===


'Required Readings''
'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]]
:* [[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 157: Line 101:
:*[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 2/10/16'' ==
[[Image:Cetacean.png | right]]
[[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)]]
:*[[media:US_Imaging_Systems_1.pdf | Ultrasound Slides (2016)]]


''Suggested Further Reading''
''Suggested Further Reading''
:* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]
:* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]
:*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]


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


==''Wednesday 2/17/16'' ==
=Week 10: Review=
[[Image:PTEN.png | left]]
==''Monday 3/13/17’’ ==
===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===
===-Final Exam Review. ‘’Speaker’’ TBD===
 
==''Wednesday 3/15/17’’ ==
===-TBD===
 
 
 
 
 
<!--
[[Image:ASL.png | right]]
===- 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.
 
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.
''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 201:
:*[[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]===
-->

Revision as of 03:47, 21 September 2016

Principles of Neuroimaging B, Winter, 2016 - 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

Monday 1/9/17’’

- Pulse Sequences. ‘’Speaker’’: TBD

Wednesday 1/11/17’’

- MR Parameters. ‘’Speaker’’: TBD

Week 2: MRI Techniques

Monday 1/16/17’’

MLK Day No Class

Wednesday 1/18/17’’

-MR Applications (MR, fMRI, DTI, ASL, Spectroscopy). ‘’Speaker’’ TBD

Week 3: Non-MR Imaging

Monday 1/23/17’’

- PET I. ‘’Speaker’’ TBD

Wednesday 1/25/17’’

- PET II. ‘’Speaker’’ TBD

PET-ring.png
PETfounders.png

Week 4: Non-MR Imaging

Monday 1/30/17’’

- Optogenetics I. ‘’Speaker’’ TBD

Wednesday 2/1/17’’

- Optogenetics II. ‘’Speaker’’ TBD

Required Readings - Please complete these readings prior to class.

Suggested Further Reading

Week 5: Multimodal Imaging & Neuroimaging Data

Monday 2/6/17’’

- Multimodal Imaging ‘’Speaker’’ TBD

Wednesday 2/8/17’’

- Neuroimaging Data: Fundamentals. ‘’Speaker’’ TBD

MIDTERM

Week 6: Neuroimaging Data

Monday 2/13/17’’

Midterm Review

‘’Wednesday 2/15/17’’

-Multivariate Analyses: Dimension Reduction. ‘’Speaker’’ TBD

Week 7: Neuroimaging Data

Monday 2/20/17’’

President’s Day Holiday No Class

Wednesday 2/22/17’’

- Multivariate Analyses: Brain Decoding ‘’Speaker’’ TBD

Week 8: Practical Brain Decoding & Connectivity

Monday 2/27/17’’

Building a BCI System

Wednesday 3/1/17’’

- Connectivity Fundamentals ‘’Speaker’’ TBD

Week 9: Neuromodulation

Monday 3/6/17’’

-TMS. ‘’Speaker’’ TBD

Wednesday 3/8/17’’

- Ultrasound. ‘’Speaker’’ TBD

'Required Readings

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

Cetacean.png

Suggested Further Reading


Week 10: Review

Monday 3/13/17’’

-Final Exam Review. ‘’Speaker’’ TBD

Wednesday 3/15/17’’

-TBD

Suggested Further Reading


Week 8: Advanced MRI methods

Monday 2/22/16

DIffusingSpheres.png

- 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

Callosum.png

- 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

Kinship.png

- Imaging Genetics. Speaker: Carrie Bearden:

Required Readings - Please complete these readings prior to class.

Suggested Further Reading


-->

Retrieved from "https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2017&oldid=3157"