Principles of Neuroimaging B - 2012: Difference between revisions

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:*[[media:ALGER_PrinciplesNeuroImaging2012DTI.pdf‎ | DTI lecture notes]]  
:*[[media:ALGER_PrinciplesNeuroImaging2012DTI.pdf‎ | DTI lecture notes]]  
:*[[media:Alger_PrinciplesNeuroImaging2012MRS.pdf‎ | Spectroscopy lecture notes.]]
:*[[media:Alger_PrinciplesNeuroImaging2012MRS.pdf‎ | Spectroscopy lecture notes.]]
'Suggested Readings''
<!--Also uploaded as Lanyon-DTIBasicsAndFuture.pdf-->
:*[http://www.intechopen.com/source/pdfs/28790/InTech-Diffusion_tensor_imaging_structural_connectivity_insights_limitations_and_future_directions.pdf DTI basics and future directions]


==''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]==
==''Friday 1/27/12'' -  TMS (tentative). ''Speakers'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu], ==
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.
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.


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:*READING
:*READING


==''Friday 2/3/12' '- Positron Emission Tomography (PET) Applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]==
==''Friday 2/3/12''- Positron Emission Tomography (PET) Applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]==
OUTLINE
OUTLINE
[[image:SmokerStroop.png|right]]
[[image:SmokerStroop.png|right]]
''Required Readings''
''Required Readings''
:*[[media:NITP_PET_applications_2-16-11.pdf | PET Applications handout]]
:*[[media:PET_applications2-08-12SM.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.]
:* [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:MukherjeeRadiopharmaceuticals.pdf | Mukherjee: Radiopharmaceuticals for Brain Imaging]]
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OUTLINE
OUTLINE
''Required Readings''
''Required Readings''
:*[[media:MultiModalNITP2012-print.pdf‎ | Multimodal imaging handout]]
:*[[media:MultiModalNITP2012SM.pdf‎ | Multimodal imaging handout]]


==''Friday 2/10/12'' - Ultrasound (''tentative''). ''Speaker'': [http://casit.ucla.edu/body.cfm?id=129 Martin Culjat]==
==''Friday 2/10/12'' - Ultrasound (''tentative''). ''Speaker'': [http://casit.ucla.edu/body.cfm?id=129 Martin Culjat]==
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=Week 6 =
=Week 6 =


==Wednesday 2/15/12 - Connectivity. "Jesse Brown"==
==Wednesday 2/15/12 - Connectivity. ''Jesse Brown''==
OUTLINE<br>
OUTLINE<br>
Connectivity in neuroimaging is a broad subject. These slides focus on resting state fMRI and DTI based connectivity methods and results.
Connectivity in neuroimaging is a broad subject. These slides focus on resting state fMRI and DTI based connectivity methods and results.
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:*[http://umcd.humanconnectomeproject.org/ UMCD]: The UCLA Multimodal Connectivity Database, a web-based repository for brain network analysis and data sharing.
:*[http://umcd.humanconnectomeproject.org/ UMCD]: The UCLA Multimodal Connectivity Database, a web-based repository for brain network analysis and data sharing.


==Friday 2/17/12 - TOPIC. "Speaker"==
==Friday 2/17/12 - Brain Stimulation. ''Alexander Bystritsky''==
OUTLINE
OUTLINE
''Required Readings''
''Required Readings''


''Suggested Further Reading''
[[media:Brainstimulation2012AB.pdf | Brain Stimulation]]
:*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 - Brain Stimulation. "Alexander Bystritsky"==
OUTLINE
''Required Readings''


''Suggested Further Reading''
''Suggested Further Reading''
:*READING
:*READING


=Week 7 =
=Week 7 =


==Wednesday 2/22/12 - Methods of Dimension Reduction. "Ariana Anderson"==
==Wednesday 2/22/12 - Methods of Dimension Reduction. ''Ariana Anderson''==
OUTLINE
OUTLINE
''Required Readings''
'''Required Readings''


''Suggested Further Reading''
''Suggested Further Reading''
:*READING
:*READING


==Friday 2/25/12 - Bayesian Statistics. "Donatello Telesca"==
==Friday 2/25/12 - Bayesian Statistics. ''Donatello Telesca''==
OUTLINE
OUTLINE
''Required Readings''
''Required Readings''
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=Week 8 =
=Week 8 =


==Wednesday 2/29/12 - TOPIC. "Speaker"==
==Wednesday 2/29/12 - CLASS IS CANCELLED FOR TODAY. SORRY==
OUTLINE
''Required Readings''
 
''Suggested Further Reading''
:*READING


==Friday 3/2/12 - TOPIC. "Speaker"==
==Friday 3/2/12 - TOPIC. "Speaker"==
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:*READING
:*READING


==Friday 3/9/12 - TOPIC. "Speaker"==
==Friday 3/9/12 - Compressive Sensing. ''Kevin Kelly - Rice University''==
OUTLINE
OUTLINE
Compressed sensing lecture by Dr. Kevin Kelly of Rice University.
''Required Readings''
''Required Readings''
*[[media:Compressed_imaging_tutorial.pdf | Compressed imaging handout]]


''Suggested Further Reading''
''Suggested Further Reading''
:*READING
:*READING


=Week 10 =
=Week 10 =


==Wednesday 3/14/12 - TOPIC. "Speaker"==
==Wednesday 3/14/12 - Single-Molecule Biological Structure: Microwave Scanning Tunneling Microscopy of Peptides. ''Shelley Claridge''==
OUTLINE
OUTLINE
''Required Readings''
''Required Readings''
:*[[media:SClaridge_14_Mar_12.pdf | Single molecule imaging]]


''Suggested Further Reading''
''Suggested Further Reading''
:*READING
:*READING


==Friday 3/16/12 - TOPIC. "Speaker"==
==Friday 3/16/12 - Machine Learning. ''Alan Yuille''==
OUTLINE
OUTLINE
''Required Readings''
''Required Readings''
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=FINALS=
=FINALS=
3/19-23/12
3/19-23/12
==''Friday 1//12'' - fMRI. ''Speaker'':
[http://www.brainmapping.org/MarkCohen Cohen]==
OUTLINE
''Required Readings''
:*[http://www.brainmapping.org/NITP/PNA/Readings/MRIforNITP.pdf slides (same as 1/3/12)]
''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 '''S'''uperconductin '''QU'''antum '''I'''nterference '''D'''evices (SQUIDs) that detect the magnetic resonance imaging signal by direct magnetometry, rather than by induction.
==''Friday 1/31/12'' - MEG and EEG. ''Speaker'': [http://www.labome.org/expert/usa/university/simpson/gregory-v-simpson-1030707.html Greg Simpson]==
[http://books.google.com/books?id=_UXLRzqrkrQC&pg=PA26&lpg=PA26&dq=greg+simpson+eeg&source=bl&ots=3w1w34NL5x&sig=M7mdZRODLpmSpqnsnLkioBGcEQo&hl=en&ei=hT6eTP_2GJHksQPu_JXWAQ&sa=X&oi=book_result&ct=result&resnum=2&ved=0CBYQ6AEwAQ#v=onepage&q=greg%20simpson%20eeg&f=false A story]
Suggested Reading
[http://www.ncbi.nlm.nih.gov/pubmed/18701689?dopt=Citation  J Neurosci. 2008 Aug 13;28(33):8268-72. "Very slow EEG fluctuations predict the dynamics of stimulus detection and oscillation amplitudes in humans". Monto S, Palva S, Voipio J, Palva JM.]
==''Friday 2/2//12'' - Ultralow field MRI. ''Speaker'': '''Konstantin Penanen''' NASA/CalTech Jet Propulsion Laboratory==
OUTLINE
[[image:miniscanGB.jpg|right]]
* [[media:Penanen_UCLA_Neuro_2011_talk.pdf | Penanen Lecture Slides]]
''Suggested Further Reading''
:*[http://www.ncbi.nlm.nih.gov/pubmed/18328753?dopt=Citation Parallel MRI at microtesla fields. Zotev VS, Volegov PL, Matlashov AN, Espy MA, Mosher JC, Kraus RH Jr. J Magn Reson. 2008 Jun;192(2):197-208. Epub 2008 Mar 6]
:*[http://www.ncbi.nlm.nih.gov/pubmed/17029228?dopt=Citation Three-dimensional prepolarized magnetic resonance imaging using rapid acquisition with relaxation enhancement. Matter NI, Scott GC, Venook RD, Ungersma SE, Grafendorfer T, Macovski A, Conolly SM. Magn Reson Med. 2006 Nov;56(5):1085-95.]
:*[http://iopscience.iop.org/0953-2048/19/5/S01/ How the SQUID was born. AH Silver. Superconductor Science and Technology Volume 19, Number 5, 2006]
:*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]==
OUTLINE
[[image:ParallaxError.jpg|right]]
''Required Readings''
:*[[media:PET_2010.pdf | PET Imaging handout]]
''Suggested Further Reading''
:*READING
==''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=
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'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=45540 Jeffry Alger]==
OUTLINE
''Required Readings''
:*[[media:Alger MRS 20100512.pdf | Spectroscopy Lecture Slides]]
''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:
:*[http://muse.jhu.edu/journals/perspectives_on_science/v007/7.2baird02.html MS Cohen and D Baird, “Why Trade?: How zones of trade support epistemic stability.” Perspective on Science,  7(2): p. 231-254. 1999.]
=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''
:*[http://en.wikipedia.org/wiki/George_Washington George Washington]
:*[http://en.wikipedia.org/wiki/Abraham_Lincoln Abraham Lincoln]
==''Wednesday 2/23/12'' - PCA, ICA, Machine learning. ''Speaker'': [http://www.stat.ucla.edu/~yuille/index.html Alan Yuille]==
OUTLINE
[[image:Probmodel.jpg|right]]
''Required Readings''
:*READING
''Suggested Further Reading''
:*READING
=Week 9 Functional Connectivity, Multimodal Integration=
WEEKLYSUMMARY
==''Friday 2/28/12'' - Functional Connectivity. ''Speaker'': [http://alenarto.bol.ucla.edu/ Agatha Lenartowicz]==
OUTLINE
''Required Readings''
:*[[media:functionalconnectivity.pdf | Functional Connectivity Lecture Slides]]
''Suggested Further Reading''
Useful software for exploring functional connectivity (correlations/bivariate/partial etc) from Susan Whitfield-Gabrieli at MIT (link courtesy of Sam):*[http://web.mit.edu/swg/software.htm]
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'': [http://www.brainmapping.org/MarkCohen Cohen]==
OUTLINE
''Required Readings''
:*[[media:Multimodal_Imaging_2011.pdf | Lecture Slides for 3-2-11]]
=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'' - ''[mailto:stm@ucla.edu Paul Weiss]  and [mailto:aandrews@mednet.ucla.edu Anne Andrews]'': [http://www.brainmapping.org/MarkCohen Cohen]==
Direct Nanoscale and Molecular Imaging.
''Required Readings''
:*[[media:AndrewsAM_Part1_09Mar2011.pdf | Andrews Lecture Slides]]
:*[[media:PWeissNITP2011.pdf‎ | Weiss Lecture Slides]]
''Suggested Further Reading''
:*READING
=Finals Week=

Latest revision as of 03:41, 16 January 2014

Principles of Neuroimaging B, Winter, 2012 - Class Schedule and Syllabus

Main course page for Principles of Neuroimaging (2010-11)
M284A Principles of Neuroimaging A

Lecture Videos

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

HahnFig1.png above: Figure 1 from Hahn, 1950

Suggested Further Reading

File:PSatSeq.jpg

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. Speaker: Jeffry Alger

OUTLINE

File:Bandwidth.jpg

Required Readings

'Suggested Readings

Friday 1/27/12 - TMS (tentative). Speakers: Allan Wu,

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

File:ParallaxError.jpg

Required Readings

Suggested Further Reading

  • READING

Friday 2/3/12- Positron Emission Tomography (PET) Applications. Speaker: Edythe London

OUTLINE

File:SmokerStroop.png

Required Readings

Suggested Further Reading

  • n/a

Week 5 fMRI and Ultrasound

Wednesday 2/8/12 - Multimodal imaging. 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

]

Week 6

Wednesday 2/15/12 - Connectivity. Jesse Brown

OUTLINE
Connectivity in neuroimaging is a broad subject. These slides focus on resting state fMRI and DTI based connectivity methods and results. Media:nitp_connectivity_02142012.pdf

Required Readings

Suggested Further Reading

  • Networks of the Brain by Olaf Sporns

Links of interest

  • INDI: the International Neuroimaging Data-sharing Initiative. A very useful source of publicly available fMRI and DTI data.
  • Human Connectome Project: The WashU-UMinn consortium will scan 1200 individuals with resting state fMRI, DSI, and structural MRI, along with MEG and 7-Tesla scanning in some cases.
  • UMCD: The UCLA Multimodal Connectivity Database, a web-based repository for brain network analysis and data sharing.

Friday 2/17/12 - Brain Stimulation. Alexander Bystritsky

OUTLINE Required Readings

Brain Stimulation

Suggested Further Reading

  • READING

Week 7

Wednesday 2/22/12 - Methods of Dimension Reduction. Ariana Anderson

OUTLINE 'Required Readings

Suggested Further Reading

  • READING

Friday 2/25/12 - Bayesian Statistics. Donatello Telesca

OUTLINE Required Readings

Suggested Further Reading

  • READING


Week 8

Wednesday 2/29/12 - CLASS IS CANCELLED FOR TODAY. SORRY

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 - Compressive Sensing. Kevin Kelly - Rice University

OUTLINE Compressed sensing lecture by Dr. Kevin Kelly of Rice University.

Required Readings

Suggested Further Reading

  • READING

Week 10

Wednesday 3/14/12 - Single-Molecule Biological Structure: Microwave Scanning Tunneling Microscopy of Peptides. Shelley Claridge

OUTLINE Required Readings

Suggested Further Reading

  • READING

Friday 3/16/12 - Machine Learning. Alan Yuille

OUTLINE Required Readings

Suggested Further Reading

  • READING

FINALS

3/19-23/12

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