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


= N.B. First draft 1-6-16 =
== This schedule ''will'' change!==
== This schedule ''will'' change!==


Line 99: Line 98:
:*
:*


=Week 4: Positron Emission Tomography=
=Week 4: Multimodal imaging=
[[Image:PET-ring.png | left]]
==''Monday 1/25/16'' ==
==''Monday 1/25/16'' ==
===Positron Emission Tomography. ''Speaker'':  [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===
===Multimodal imaging. ''Speaker'':  [http://www.brainmapping.org/MarkCohen MarkCohen]===
Handouts distributed in class.
Handouts distributed in class.


''Required Readings'' - Please complete these readings prior to class.
''Required Readings'' - Please complete these readings prior to class.
:*[[media:PET_2015_SM.pdf | Dr. Dahlbom's PET handout]]
:*[[media:MultimodalNITP.pdf | slides handout]]


<!--
<!--
Line 117: Line 115:
:*
:*


[[Image:PETfounders.png | right]]
==''Wednesday 1/27/16'' ==
==''Wednesday 1/27/16'' ==
===PET applications. ''Speaker'':  [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===
===Class canceled.===
''Required Readings'' - Please complete these readings prior to class.
:*[[Media:NITP_PET_2-23-15_SM.pdf | Dr. Edythe London PET Slides]]
''Suggested Further Reading''


=Week 5: tbd=
=Week 5: Positron Emission Tomography=
[[Image:PET-ring.png | left]]
==''Monday 2/1/16'' ==
==''Monday 2/1/16'' ==
===- Topic. ''Speaker'': ===
===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.
''Required Readings'' - Please complete these readings prior to class.
:*
:*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]
 
<!--
<!--
:*[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.]
Line 139: Line 136:
:*
:*


[[Image:PETfounders.png | right]]


==''Wednesday 2/3/16'' ==
==''Wednesday 2/3/16'' ==
===- Topic. ''Speaker'': ===
===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===
 
''Required Readings'' - Please complete these readings prior to class.
''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'''
<!--
:*[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 6: tbd=
=Week 6: Brain Stimulation and Ultrasound=
==''Monday 2/8/16'' ==
==''Monday 2/8/16'' ==
===- Topic. ''Speaker'': ===
===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]


''Required Readings'' - Please complete these readings prior to class.
:*
<!--
:*[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''
:*
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'' ==
==''Wednesday 2/10/16'' ==
===- Topic. ''Speaker'': ===
[[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)]]


''Required Readings'' - Please complete these readings prior to class.
:*
<!--
:*[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''
:*
:* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]
:*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]


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


==''Wednesday 2/17/16'' ==
==''Wednesday 2/17/16'' ==
===- Optical Neuroimaging and Optogenetics. ''Peyman Golshani'': ===
[[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: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''
:*
:*
Line 203: Line 183:
=Week 8: Advanced MRI methods=
=Week 8: Advanced MRI methods=
==''Monday 2/22/16'' ==
==''Monday 2/22/16'' ==
===- Diffusion MRI. ''Ben Ellingson'': ===
[[Image:DIffusingSpheres.png | left]]
===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&action=detail&ref=18 Ben Ellingson]===
''Required Readings''
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 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14
''Suggested Further Reading''
:*[[media:DTIHageman.pdf | Hageman DTI Slides]]
:*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]
:*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]


''Required Readings'' - Please complete these readings prior to class.
:Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):
:*
:*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]
<!--
:*[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.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''
:*


==''Wednesday 2/25/16'' ==
==''Wednesday 2/25/16'' ==
===- Brain Morphometry. ''Roger Woods'': ===
[[Image:Callosum.png | right]]
===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===
''Required Readings'' - Please complete these readings prior to class.
:*[[media:M284B_Woods.pdf‎ | Dr. Woods' slides]]


''Required Readings'' - Please complete these readings prior to class.
:*
<!--
:*[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.ncbi.nlm.nih.gov/pubmed/12667854 *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=
=Week 9: MR Spectroscopy=
==''Monday 2/29/16'' ==
==''Monday 2/29/16'' ==
===- Clinical Spectroscopy. ''Joseph O'Neill'': ===
No class
 
==''Wednesday 3/2/16'' ==
=== Spectroscopy fundamentals. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===


''Required Readings'' - Please complete these readings prior to class.
''Required Readings'' - Please complete these readings prior to class.
:*
:*[[media:ONeill2016Spectro.pdf‎ | Dr. O'Neill's 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''
:*


==''Wednesday 3/2/16'' ==
===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&action=detail&ref=65 Albert Thomas] ===
===- Spectroscopic Methods. ''Albert Thomas'': ===


''Required Readings'' - Please complete these readings prior to class.
''Required Readings'' - Please complete these readings prior to class.
:*
:*[[media:M284B_AThomas030216.pdf‎ | Dr. Thomas' 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.ncbi.nlm.nih.gov/pubmed/23292856 SA Wijtenburg, LM Rowland, RA Edden and PB Barker, “Reproducibility of brain spectroscopy at 7T using conventional localization and spectral editing techniques.” J Magn Reson Imaging,  38(2): p. 460-467. 2013. PMCID: PMC3620961]
:* [http://www.ncbi.nlm.nih.gov/pubmed/20574964 S Lipnick, G Verma, S Ramadan, J Furuyama and MA Thomas, “Echo planar correlated spectroscopic imaging: implementation and pilot evaluation in human calf in vivo.” Magn Reson Med,  64(4): p. 947-956. 2010. PMCID: PMC2946523]
:* [http://www.ncbi.nlm.nih.gov/pubmed/22505247 JK Furuyama, NE Wilson, BL Burns, R Nagarajan, DJ Margolis and MA Thomas, “Application of compressed sensing to multidimensional spectroscopic imaging in human prostate.” Magn Reson Med,  67(6): p. 1499-1505. 2012.]


=Week 10: Multimodal Methods=
=Week 10: Multimodal Methods / Course wrap up=
==''Monday 3/7/16'' ==
==''Monday 3/7/16'' ==
===- Imaging Genetics. ''Carrie Bearden'': ===
[[Image:Kinship.png | right]]
===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===
''Required Readings'' - Please complete these readings prior to class.
:*[[media:Bearden_NITP2_2016-3-4.pdf | Dr. Bearden's slides]]


''Required Readings'' - Please complete these readings prior to class.
:*
<!--
:*[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''
:*
:*[[media:Carter-Genomics.pdf | ''Enhancing the Informativeness and Replicability of Imaging Genomics Studies'' Carter et al.]]
:*[[media:Flint_and_Geschwind.pdf | ''Genetics and genomics of psychiatric disease'' Flint and Geschwind]]


==''Wednesday 3/9/16'' ==
==''Wednesday 3/9/16'' ==
===- Multimodal imaging approaches.  ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
===- Course wrap up and review.  ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
 
''Required Readings'' - Please complete these readings prior to class.
:*
<!--
:*[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''
:*

Latest revision as of 00:08, 10 March 2016

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

This schedule will change!

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

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 1/4/16

- MRI Contrast. Mark Cohen: 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

Required Readings

Suggested Further Reading

HahnFig1.png

}

Figure 1 from Hahn, 1950

Wednesday 1/6/16

- MRI Image Formation and fMRI. Mark Cohen: Mark Cohen

Week 2: MRI Techniques

Monday 1/11/16

ASL.png

- Measurement of Blood Flow by MRI. Danny JJ Wang: [1]

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.

Suggested Further Reading

Wednesday 1/13/16

- More MRI. Mark Cohen: Mark Cohen

Required Readings - Please complete these readings prior to class.

Suggested Further Reading

Week 3: tbd

Monday 1/18/16

- MLK School Holiday

Wednesday 1/20/16

- tbd. Speaker: Mark Cohen

Abstract

Required Readings - Please complete these readings prior to class.

Suggested Further Reading

Week 4: Multimodal imaging

Monday 1/25/16

Multimodal imaging. Speaker: MarkCohen

Handouts distributed in class.

Required Readings - Please complete these readings prior to class.

Suggested Further Reading

Wednesday 1/27/16

Class canceled.

Week 5: Positron Emission Tomography

PET-ring.png

Monday 2/1/16

Positron Emission Tomography. Speaker: Magnus Dahlboun

Handouts distributed in class.

Required Readings - Please complete these readings prior to class.

Suggested Further Reading

PETfounders.png

Wednesday 2/3/16

PET applications. Speaker: Edythe London

Required Readings - Please complete these readings prior to class.

Suggested Further Reading

Week 6: Brain Stimulation and Ultrasound

Monday 2/8/16

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 2/10/16

Cetacean.png

Ultrasound. Speaker: George Saddik

Required Readings

Suggested Further Reading

Week 7: Optical neuroimaging and optogenetics

Monday 2/15/16

- President's Day - School holiday:

Wednesday 2/17/16

PTEN.png

- Optical Neuroimaging and Optogenetics. Speaker: Peyman Golshani:

Required Readings - Please complete these readings prior to class.

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

Wednesday 3/9/16

- Course wrap up and review. Mark Cohen: Mark Cohen