Principles of Neuroimaging B - 2012: Difference between revisions
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==''Wednesday 1/ | ==''Wednesday 1/11/12'' - MRI. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]== | ||
OUTLINE | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
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[[image:PSatSeq.jpg|right]] | [[image:PSatSeq.jpg|right]] | ||
==''Friday 1/ | ==''Friday 1/13/12'' - MRI II. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]== | ||
OUTLINE | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
Line 53: | Line 53: | ||
=Week 2 MRI Applications= | =Week 2 MRI Applications= | ||
==''Wednesday 1/ | ==''Wednesday 1/18/12'' - Connectivity. ''Speaker'': [http://ccn.ucla.edu/~jbrown/ Jesse Brown]== | ||
OUTLINE | |||
''Required Readings'' | |||
:* | |||
''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] | |||
: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] | |||
''Suggested Further Reading'' | |||
:*READING | |||
==''Friday 1/20/12'' - Advanced MRI Pulse Sequences. ''Speaker'': [http://www.radiology.ucla.edu/dcvi/html/people/Ennis.html Daniel Ennis]== | |||
=Week 3 Advanced MRI Applications and TMS= | |||
==''Wednesday 1/25/12'' - Diffusion (''tentative''). ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=45540 Jeffry Alger]== | |||
OUTLINE | OUTLINE | ||
[[image:Bandwidth.jpg|right]] | [[image:Bandwidth.jpg|right]] | ||
''Required Readings'' | ''Required Readings'' | ||
:* | :* | ||
==''Friday 1/27/12'' - TMS (tentative). ''Speakers'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu], [http://www.anxiety.org/about/alexander_bystritsky Alexander Bystritsky]== | |||
Transcranial Magnetostimulation is fundamentally different than the other technologies we have explored, in that it is used specifically to ''alter'' ongoing brain activity. While not exactly an imaging method, the TMS instrument is image-guided and uses tomographic placement. | |||
'Required Readings'' | |||
:* [[media:TMS_Wu_2011.pdf | Wu 2011 Lecture slides]] | |||
:* [[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'' | |||
:* [[media:WuTMS-05-04-10.pdf | Handout for Wu TMS Lecture, 2010]] | |||
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] | |||
=Week 4 PET= | |||
==''Wednesday 2/1/12'' - Positron Emission Tomography (PET). ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlbom]== | |||
OUTLINE | |||
[[image:ParallaxError.jpg|right]] | |||
''Required Readings'' | |||
:*[[media:PET_2010.pdf | PET Imaging handout]] | |||
''Suggested Further Reading'' | |||
:*READING | |||
==''Friday 2/3/12' '- Positron Emission Tomography (PET) Applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]== | |||
OUTLINE | |||
[[image:SmokerStroop.png|right]] | |||
''Required Readings'' | |||
:*[[media:NITP_PET_applications_2-16-11.pdf | PET Applications handout]] | |||
:* [http://www.ncbi.nlm.nih.gov/pubmed/3099392?dopt=Citation “Mapping human brain monoamine oxidase A and B with <sup><small>11</small></sup>C-labeled suicide inactivators and PET.” Science, 235(4787): p. 481-485. 1987.] | |||
:* [[media:MukherjeeRadiopharmaceuticals.pdf | Mukherjee: Radiopharmaceuticals for Brain Imaging]] | |||
:* [[media:Martinez_Drugs_of_Abuse.pdf | Imaging Neurotransmitter Release by Drugs of Abuse, Diana Martinez and Rajesh Narendran]] | |||
''Suggested Further Reading'' | |||
:*n/a | |||
=Week 5 fMRI and Ultrasound= | |||
==''Wednesday 2/8/12'' - fMRI. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]== | |||
OUTLINE | |||
''Required Readings'' | |||
:*[[media:MRIforPNIB.pdf | MRI Slides (same as 1/4/12)]] | |||
==''Friday 2/10/12'' - Ultrasound (''tentative''). ''Speaker'': [http://casit.ucla.edu/body.cfm?id=129 Martin Culjat]== | |||
OUTLINE | |||
Ultrasound is one of the earliest means of seeing into the body. Until recently, however, seeing into the brain has been very poor. Recent advances are improving on this. | |||
''Required Readings'' | |||
:* | |||
''Suggested Further Reading'' | |||
:* | |||
=Everything below here is entirely tentative= | |||
=Week 6 = | |||
==Wednesday 2/15/12 - TOPIC. "Speaker"== | |||
OUTLINE | |||
''Required Readings'' | |||
''Suggested Further Reading'' | |||
:*READING | |||
==Friday 2/17/12 - TOPIC. "Speaker"== | |||
OUTLINE | |||
''Required Readings'' | |||
''Suggested Further Reading'' | |||
:*READING | |||
=Week 6 = | |||
==Wednesday 2/15/12 - TOPIC. "Speaker"== | |||
OUTLINE | |||
''Required Readings'' | |||
''Suggested Further Reading'' | |||
:*READING | |||
==Friday 2/17/12 - TOPIC. "Speaker"== | |||
OUTLINE | |||
''Required Readings'' | |||
''Suggested Further Reading'' | |||
:*READING | |||
=Week 6 = | |||
==Wednesday 2/15/12 - TOPIC. "Speaker"== | |||
OUTLINE | |||
''Required Readings'' | |||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:*READING | :*READING | ||
==Friday 2/17/12 - TOPIC. "Speaker"== | |||
OUTLINE | |||
''Required Readings'' | |||
== | ''Suggested Further Reading'' | ||
:*READING | |||
=Week 7 = | |||
==Wednesday 2/22/12 - TOPIC. "Speaker"== | |||
OUTLINE | |||
''Required Readings'' | |||
''Suggested Further Reading'' | |||
:*READING | |||
==Friday 2/25/12 - TOPIC. "Speaker"== | |||
OUTLINE | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:*READING | :*READING | ||
== | =Week 8 = | ||
==Wednesday 2/29/12 - TOPIC. "Speaker"== | |||
OUTLINE | |||
''Required Readings'' | |||
''Suggested Further Reading'' | |||
:*READING | |||
==Friday 3/2/12 - TOPIC. "Speaker"== | |||
OUTLINE | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:* | :*READING | ||
=Week 9 = | |||
==Wednesday 3/7/12 - TOPIC. "Speaker"== | |||
OUTLINE | |||
''Required Readings'' | |||
''Suggested Further Reading'' | |||
:*READING | |||
= | ==Friday 3/9/12 - TOPIC. "Speaker"== | ||
OUTLINE | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:* | :*READING | ||
=Week 10 = | |||
== | ==Wednesday 3/14/12 - TOPIC. "Speaker"== | ||
OUTLINE | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:*READING | :*READING | ||
= | ==Friday 3/16/12 - TOPIC. "Speaker"== | ||
OUTLINE | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:*READING | :*READING | ||
==''Friday | =FINALS= | ||
3/19-23/12 | |||
==''Friday 1//12'' - fMRI. ''Speaker'': | |||
[http://www.brainmapping.org/MarkCohen Cohen]== | |||
OUTLINE | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
:*[http://www.brainmapping.org/NITP/PNA/Readings/MRIforNITP.pdf slides (same as 1/3/12)] | |||
:* [http://www. | |||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:* | :*READING | ||
Dr. Simpson is a leading expert in the use of scalp electrophysiology (EEG and MEG) to explore the dynamical processes of the human brain, and the integration of activity across cortex in complex human behaviors. Notably, the MEG instrument also uses the SQUID technology | Dr. Simpson is a leading expert in the use of scalp electrophysiology (EEG and MEG) to explore the dynamical processes of the human brain, and the integration of activity across cortex in complex human behaviors. Notably, the MEG instrument also uses the SQUID technology | ||
Line 157: | Line 293: | ||
:*John Clarke, SQUIDs: Scientific American, August 1994. | :*John Clarke, SQUIDs: Scientific American, August 1994. | ||
==''Friday 2/7/12'' - Positron Emission Tomography (PET). ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlbom]== | ==''Friday 2/7/12'' - Positron Emission Tomography (PET). ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlbom]== | ||
Line 172: | Line 304: | ||
==''Wednesday 2/9/12'' - Transcranial Magneto Stimulation (TMS). ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]== | ==''Wednesday 2/9/12'' - Transcranial Magneto Stimulation (TMS). ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]== | ||
=Week 7 Spectroscopy and PET= | =Week 7 Spectroscopy and PET= |
Revision as of 19:48, 4 January 2012
Principles of Neuroimaging B, Winter, 2012 - Class Schedule and Syllabus
Lecture Videos
- Friday 1-3-11 - MR Signals and Contrast, Speaker Mark Cohen
- Wednesday 1-5-11 - MR Spatial Encoding I, Speaker Mark Cohen
- Wednesday 1-5-11 - MR Spatial Encoding II, Speaker Mark Cohen
- Friday 1-10-11 - fMRI and Diffusion, Speaker Mark Cohen
- Wednesday 1-12-11 - fMRI Image Quality and Artifacts, Speaker Mark Cohen
- Friday 1-24-11 - Experimental Design I, Speaker Susan Bookheimer
- Friday 1-24-11 - Experimental Design II, Speaker Susan Bookheimer
- Wednesday 1-26-11 - DTI, Speaker Nathan Hageman
- Friday 1-31-11 - MEG/EEG, Speaker Gregory Simpson
- Wednesday 2-2-11 - Ultra Low Field MRI, Speaker Konstantin Penanen
- Wednesday 2-9-11 - TMS, Speaker Allan Wu
- Friday 2-14-11 - MRS, Speaker Jeff Algers
Week 1 Magnetic Resonance Imaging
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
Wednesday 1/11/12 - MRI. Speaker: Cohen
OUTLINE Required Readings
- MRI Slides
- These notes by Joseph Hornak are highly professional and complete coverage of MRI.
- eMRI is another excellent online MRI learning resource
- Erwin Hahn - Spin Echoes: Essential reading for the MRI community
above: Figure 1 from Hahn, 1950
Suggested Further Reading
Friday 1/13/12 - MRI II. Speaker: Cohen
OUTLINE Required Readings
Suggested Further Reading
- READING
WEEKLY SUMMARY
Week 2 MRI Applications
Wednesday 1/18/12 - Connectivity. Speaker: Jesse Brown
OUTLINE Required Readings
Suggested Further Reading
- Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):
Suggested Further Reading
- READING
Friday 1/20/12 - Advanced MRI Pulse Sequences. Speaker: Daniel Ennis
Week 3 Advanced MRI Applications and TMS
Wednesday 1/25/12 - Diffusion (tentative). Speaker: Jeffry Alger
OUTLINE
Required Readings
Friday 1/27/12 - TMS (tentative). Speakers: Allan Wu, Alexander Bystritsky
Transcranial Magnetostimulation is fundamentally different than the other technologies we have explored, in that it is used specifically to alter ongoing brain activity. While not exactly an imaging method, the TMS instrument is image-guided and uses tomographic placement.
'Required Readings
Suggested Further Reading
Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:
Week 4 PET
Wednesday 2/1/12 - Positron Emission Tomography (PET). Speaker: Magnus Dahlbom
OUTLINE
Required Readings
Suggested Further Reading
- READING
Friday 2/3/12' '- Positron Emission Tomography (PET) Applications. Speaker: Edythe London
OUTLINE
Required Readings
Suggested Further Reading
- n/a
Week 5 fMRI and Ultrasound
Wednesday 2/8/12 - fMRI. Speaker: Cohen
OUTLINE Required Readings
Friday 2/10/12 - Ultrasound (tentative). Speaker: Martin Culjat
OUTLINE
Ultrasound is one of the earliest means of seeing into the body. Until recently, however, seeing into the brain has been very poor. Recent advances are improving on this.
Required Readings
Suggested Further Reading
Everything below here is entirely tentative
Week 6
Wednesday 2/15/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Friday 2/17/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Week 6
Wednesday 2/15/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Friday 2/17/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Week 6
Wednesday 2/15/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Friday 2/17/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Week 7
Wednesday 2/22/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Friday 2/25/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Week 8
Wednesday 2/29/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Friday 3/2/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Week 9
Wednesday 3/7/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Friday 3/9/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Week 10
Wednesday 3/14/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
Friday 3/16/12 - TOPIC. "Speaker"
OUTLINE Required Readings
Suggested Further Reading
- READING
FINALS
3/19-23/12
==Friday 1//12 - fMRI. Speaker:
Cohen==
OUTLINE
Required Readings
Suggested Further Reading
- READING
Dr. Simpson is a leading expert in the use of scalp electrophysiology (EEG and MEG) to explore the dynamical processes of the human brain, and the integration of activity across cortex in complex human behaviors. Notably, the MEG instrument also uses the SQUID technology
Konstantin Penanen, together with Inseob Hahn and Byeong Ho Eom, have created a highly unusual MR imaging instrument that collects data in a magnetic field less than that of the earth. The tool uses Superconductin QUantum Interference Devices (SQUIDs) that detect the magnetic resonance imaging signal by direct magnetometry, rather than by induction.
Friday 1/31/12 - MEG and EEG. Speaker: Greg Simpson
Suggested Reading
Friday 2/2//12 - Ultralow field MRI. Speaker: Konstantin Penanen NASA/CalTech Jet Propulsion Laboratory
OUTLINE
Suggested Further Reading
- John Clarke, SQUIDs: Scientific American, August 1994.
Friday 2/7/12 - Positron Emission Tomography (PET). Speaker: Magnus Dahlbom
OUTLINE
Required Readings
Suggested Further Reading
- READING
Wednesday 2/9/12 - Transcranial Magneto Stimulation (TMS). Speaker: Allan Wu
Week 7 Spectroscopy and PET
Both PET and MRI are means of localizing specific molecular species. MRI has lower sensitivity but good quantitative accuracy and the ability to simultaneously image and study multiple molecules and compounds. Our lecture on PET will consider the actual imaging device, its sensitivity and its limitations.
Friday 2/14/12 - Magnetic Resonance Spectroscopy. Speaker: Jeffry Alger
OUTLINE Required Readings
Suggested Further Reading A question came up from the audience about the problem of simultaneously space and chemical shift by frequency. For an amusing story about the problem, you might want to read:
Week 8 Machine Learning
This week we will look at modern and advanced analytic methods broadly called machine learning, or statistical pattern analysis. These methods are of great interest in the imaging community as they offer high sensitivity, the ability to explore activity at the systems level and the potential for predictive analysis and brain reading.
Friday 2/21/12 - Presidents Day.
Suggested Further Reading
Wednesday 2/23/12 - PCA, ICA, Machine learning. Speaker: Alan Yuille
OUTLINE
Required Readings
- READING
Suggested Further Reading
- READING
Week 9 Functional Connectivity, Multimodal Integration
WEEKLYSUMMARY
Friday 2/28/12 - Functional Connectivity. Speaker: Agatha Lenartowicz
OUTLINE
Required Readings
Suggested Further Reading
Useful software for exploring functional connectivity (correlations/bivariate/partial etc) from Susan Whitfield-Gabrieli at MIT (link courtesy of Sam):*[1]
And additional readings in defense of DCM (other key papers are referenced in the slides)
Lee et al 2006 "Large-scale neural models and dynamic causal modelling"
David et al 2008 "Identifying Neural Drivers with Functional MRI: An Electrophysiological Validation"
Schuyler et al 2010 "Dynamic Causal Modeling applied to fMRI data shows high reliability"
Wednesday 3/2/12 - Multimodal Integration. Speaker: Cohen
OUTLINE Required Readings
Week 10 tbd
This week is presently left open for added topics and makeup as needed.
Friday 3/7/12 - Final Distributed. MSC
OUTLINE Required Readings
- READING
Suggested Further Reading
- READING
Wednesday 3/9/12 - Paul Weiss and Anne Andrews: Cohen
Direct Nanoscale and Molecular Imaging. Required Readings
Suggested Further Reading
- READING