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 | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
:* | :* | ||
''Suggested Further Reading'' | ''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. | :*[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. | |||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:*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. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=45540 Jeffry Alger]== | |||
OUTLINE | OUTLINE | ||
[[image:Bandwidth.jpg|right]] | |||
''Required Readings'' | ''Required Readings'' | ||
:* | :*[[media:ALGER_PrinciplesNeuroImaging2012DTI.pdf | DTI 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], == | ||
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]] | ||
:*[http://www. | :* [[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'' | ''Suggested Further Reading'' | ||
:* [[media:WuTMS-05-04-10.pdf | Handout for Wu TMS Lecture, 2010]] | |||
:*[[media: | |||
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 | =Week 4 PET= | ||
==''Wednesday 2/1/12'' - Positron Emission Tomography (PET). ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlbom]== | ==''Wednesday 2/1/12'' - Positron Emission Tomography (PET). ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlbom]== | ||
OUTLINE | OUTLINE | ||
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[[image:SmokerStroop.png|right]] | [[image:SmokerStroop.png|right]] | ||
''Required Readings'' | ''Required Readings'' | ||
:*[[media: | :*[[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]] | ||
Line 129: | Line 121: | ||
:*n/a | :*n/a | ||
=Week 5 fMRI and Ultrasound= | |||
==''Wednesday 2/8/12'' - Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]== | |||
OUTLINE | |||
''Required Readings'' | |||
:*[[media:MultiModalNITP2012SM.pdf | Multimodal imaging handout]] | |||
==''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 Reading | ''Suggested Further Reading'' | ||
:*[http://www.jultrasoundmed.org/content/24/12/1671.full.pdf+html “Intraoperative sonography for neurosurgery.” J Ultrasound Med, 24(12): p. 1671-1682. 2005 | |||
] | |||
:*[http://folk.ntnu.no/htorp/Undervisning/MEDT8002/litteratur/NURO51020402.pdf Brain operations guided by real-time two-dimensional ultrasound: new possibilities as a result of improved image quality.” Neurosurgery, 51(2): p. 402-411; discussion 411-402. 2002] | |||
:*[[media:biomed298 | Biomed 298 Design of Medical Ultrasound]] | |||
=Week 6 = | |||
== | ==Wednesday 2/15/12 - Connectivity. ''Jesse Brown''== | ||
OUTLINE | OUTLINE<br> | ||
[[ | 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]] | |||
* [[media: | ''Required Readings'' | ||
:*[[media:Bullmore_Sporns_NatRevNeuro_2009.pdf | Review of connectivity]] | |||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:* | :*<i>Networks of the Brain</i> by Olaf Sporns | ||
:*[http:// | ''Links of interest'' | ||
:*[http://fcon_1000.projects.nitrc.org/ INDI]: the International Neuroimaging Data-sharing Initiative. A very useful source of publicly available fMRI and DTI data. | |||
:*[http://www.humanconnectome.org/ 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. | |||
:*[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 - Brain Stimulation. ''Alexander Bystritsky''== | |||
OUTLINE | |||
''Required Readings'' | |||
: | [[media:Brainstimulation2012AB.pdf | Brain Stimulation]] | ||
''Suggested Further Reading'' | |||
:*READING | |||
=Week 7 = | |||
== | ==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''== | ||
'Required Readings'' | OUTLINE | ||
''Required Readings'' | |||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:*READING | |||
=Week 8 = | |||
==Wednesday 2/29/12 - CLASS IS CANCELLED FOR TODAY. SORRY== | |||
= | ==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 | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:*READING | :*READING | ||
==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 | |||
=Week 10 = | |||
== | ==Wednesday 3/14/12 - Single-Molecule Biological Structure: Microwave Scanning Tunneling Microscopy of Peptides. ''Shelley Claridge''== | ||
OUTLINE | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
:*[[media: | :*[[media:SClaridge_14_Mar_12.pdf | Single molecule imaging]] | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:*READING | :*READING | ||
== | ==Friday 3/16/12 - Machine Learning. ''Alan Yuille''== | ||
OUTLINE | |||
''Required Readings'' | ''Required Readings'' | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:*READING | :*READING | ||
= | =FINALS= | ||
3/19-23/12 |
Latest revision as of 03:41, 16 January 2014
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. Speaker: Jeffry Alger
OUTLINE
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
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 - 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
- [http://www.jultrasoundmed.org/content/24/12/1671.full.pdf+html “Intraoperative sonography for neurosurgery.” J Ultrasound Med, 24(12): p. 1671-1682. 2005
]
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
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