Principles of Neuroimaging B - 2014: Difference between revisions

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*[[Notes for Instructors]]
*[[Notes for Instructors]]


 
=Week 1 - A late start=
==[http://doodle.com/pvskg5w3kh6wa86n Class Time Doodle Link]==
==''Monday 1/6/14'', ''Wednesday 1/8/14'' - No Class==
 
==[http://www.doodle.com/f7a8mssf4y5hik8h Help Session Doodle Link]==
 
=Week 1 Magnetic Resonance Imaging=
==''Monday 1/6/14'', "Wednesday 1/8/14" - No Class==


=Week 2 - in class lab project=
=Week 2 - in class lab project=
==''Monday 1/13/14'', "Wednesday 1/15/14" - EKG Circuit Build ''Speaker'': Cameron Rodriguez==
==''Monday 1/13/14, Wednesday 1/15/14'' ==
===- EKG Circuit Build. ''Speaker'': Cameron Rodriguez===


=Week 3 Magnetic Resonance Imaging=
=Week 3 - Swine flu and MRI=
==''Monday 1/20/14''==
===Class canceled due to flu. Sorry===
==''Wednesday 1/22/14''==
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
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
==
 
OUTLINE
OUTLINE
''Required Readings''
''Required Readings''
:*[[media:MRIforPNIB.pdf‎ | MRI Slides]]
:*[[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.
:*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.
:*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource
:*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource
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''Suggested Further Reading''
''Suggested Further Reading''
[[image:PSatSeq.jpg|right]]
[[image:PSatSeq.jpg|right]]
=Week 4 - Magnetic Resonance Imaging=


=="Monday 1/20/14 - MRI I. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]==
==''Monday 1/27/1'' - MRI==
===-MRI I ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]===
''Required Readings''
''Required Readings''
:*[[media:MRIforPNIB.pdf‎ | MRI Slides for three lectures]
:*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]
==''Wednesday 1/22/14'' - MRI II. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]==
==''Wednesday 1/29/14'' - MRI II. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]==
OUTLINE
 
 
 
''Suggested Further Reading''
:*READING
 
<!-- :*[[media:PS1-PNIB2011.pdf | Problem Set 1]] -->
 
 
=Week 2 MRI Applications=
 
==''Monday 1/14/13'' - Functional MRI. ''Speaker'':  [http://www.brainmapping.org/MarkCohen Cohen]==
 
===Videos - Please Right Click and Save rather than Stream ===


:*[http://ccn.ucla.edu/media/20130114-part1.mp4 Lecture Part 1]
=Week 5 MRI and multimodal imaging=
:*[http://ccn.ucla.edu/media/20130114-part2.mp4 Lecture Part 2]
==''Monday 2/3/14''==
===MRI (fMRI) III. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]===
==''Wednesday 2/5/14''==
===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]===
:* [[Media:MultiModalNITP2013-sm.pdf | Multimodal neuroimaging lecture slides]]


==''Wednesday 1/16/13'' - Functional MRI. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]==
=Week 6 Diffusion and PET=
OUTLINE
==''Monday 2/10/14''==
===Diffusion imaging. ''Speaker'': Ben Ellingson===
''Required Readings''
''Required Readings''
:*
Slides should be up soon.
 
:*[[media:1_DiffusionMRI_Methods_v1.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14
''Suggested Further Reading''
''Suggested Further Reading''
:*[[Media:DTIHageman.pdf | Hageman DTI Slides]]
:*[[media:DTIHageman.pdf | Hageman DTI Slides]]
:*[[Media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]
:*[[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]
:*[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]


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:*[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.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''
==''Wednesday 2/12/14''==
:*READING
===Positron Emission Tomography. ''Speaker'':  [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===
 
Handouts distributed in class.
=Week 3 =
 
==''Monday 1/21/13'' - NO CLASS - Martin Luther King Day ==
 
==''Wednesday 1/23/13'' - Functional MRI. ''Speaker'':  [http://www.brainmapping.org/MarkCohen Cohen]==
 
=Week 4 PET Imaging=
 
==''Monday 1/28/13'' - PET. ''Speaker'':  [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]==


:*[[Media:PS1_–_PNIB2013.pdf‎ | Problem Set 1 Due 02/06/2013 by 5PM]]
=Week 7=
==''Monday 2/17/14'' Presidents Day - No class==
==''Wednesday 2/19/14''==


==''Wednesday 1/30/13'' - PET. ''Speaker'':  [http://www.semel.ucla.edu/profile/edythe-london Edythe London]==
=Week 8 Transcranial Magnetostimulation and PET applications=
 
==''Monday 2/24/14''==
:*[[Media:NITP_PET_1-30-13.pdf | Dr. Edythe London PET Slides]]
===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===
 
=Week 5 =
 
==''Monday 2/4/13'' -  . ''Speaker'':  ==
 
 
==''Wednesday 2/6/13'' - No Lecture - Optional Help Session  ==
 
 
=Week 6 =
 
==''Monday 2/11/13'' -  Neuromodulation . ''Speaker'':  [http://www.semel.ucla.edu/profile/alexander-bystritsky Alexander Bystritsky] ==
 
 
 
==''Wednesday 2/13/13'' - . ''Speaker'':  ==
 
=Week 7 =
 
==''Monday 2/18/13'' - NO CLASS - Presidents Day ==
 
==''Wednesday 2/20/13'' - Transcranial Magneto Stimulation (TMS). ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]==
'Required Readings''
'Required Readings''
:* [[media:WuTMSFeb2013.pdf | Wu 2013 Lecture slides]]
:* [[media:Wu-TMS-2014-02-24-sm.pdf | Wu Lecture slides]]
:* [[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]


''Suggested Further Reading''
''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:
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]
:*[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 8 =
==Wednesday 2/26/1.==
===PET applications. ''Speaker'':  [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===


==''Monday 2/25/13'' - Functional Connectivity. ''Speaker'': Jesse Brown ==
:*[[Media:London_NITP_PET_2-26-14_sm.pdf | Dr. Edythe London PET Slides]]


=Week 9 - Spectroscopy=
==''Monday 3/3/14'' - Class canceled==
==''Wednesday 3/5/14''==
===Spectroscopy. ''Speaker:'' [http://radiology.ucla.edu/body.cfm?id=48&action=detail&ref=65 Albert Thomas]===
Handouts distributed in class


==''Wednesday 2/27/13'' - Simultaneous multimodal neuroimaging. ''Speaker'': Mark Cohen ==
=Week 10 - Compressed sensing and finals=
==''Monday 3/10/14''==
===Compressed Sensing. ''Speaker:'' [http://www.math.ucla.edu/~yanm/ Ming Yan]===
:*[[IntroductionToCS.pdf | Ming Yan's slides on compressive sensing]]


=== Room CHS 13-105, Near the biomedical library ===
To access the slides from the course web site listed on his handout, The username is "caame654", and password is "dense".
 
:* [[Media:MultiModalNITP2013_sm.pdf‎ | Multimodal neuroimaging lecture slides]]
''Suggested Further Reading''
 
:*READING
=Week 9 =
::[http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4472240 ''"An Introduction to Compressive Sampling"'' EJ Candes, MB Watkin, IEEE Signal Processing Magazine, March, 2008] <-- Mark's favorite. This is a good overview of the field.
 
::[http://onlinelibrary.wiley.com/store/10.1002/mrm.21391/asset/21391_ftp.pdf?v=1&t=hsp7jehy&s=27fb10a08b071dd33590829f6d3101481109fae8&systemMessage=Wiley+Online+Library+will+be+disrupted+Saturday%2C+15+March+from+10%3A00-12%3A00+GMT+%2806%3A00-08%3A00+EDT%29+for+essential+maintenance ''"Sparse MRI: The Application of Compressed Sensing for Rapid MR Imaging"'' M. Lustig, D. Donoho, J.M. Pauly, Magn. Reson. Med 58:1182–1195, 2007] Lustig demonstrates each step in the process with examples using MRI.
==''Monday 3/4/13'' - Multi-voxel Pattern Analysis . ''Speaker'': Jesse Rissman==
::[http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=1614066 ''"Compressed Sensing"'', D. Donoho, IEEE Trans. Inform. Theory 52:1289, 2006] One of the more accessible formal discussions of CS
 
::[http://dsp.rice.edu/cs Rice University Compressed Sensing Resources]. A repository of scholarly work on CS.
:* [[Media:Rissman_MVPA_for_Principles_of_Neuroimaging_course_(March_2013).pdf‎ | Multi-voxel Pattern Analysis Lecture Slides]]
 
=== Room CHS 13-105 ===
 
==''Wednesday 3/6/13'' - . ''Speaker'': Martin Monti  ==
 
:* [[Media:NITP2012_MMonti_01_ExperimentalDesign_Advanced_print.pdf‎ | Advanced Experimental Design Lecture Slides]]
 
=== Room CHS 16-154 ===
 
=Week 10 =
 
==''Monday 3/11/13'' - NO CLASS -  ==
 
==''Wednesday 3/13/13'' - . ''Speaker'': Agatha Lenartowicz ==
 
:* [[Media:EEGNeurophys_130313.pdf | EEG Neurophysiology Lecture Slides]]
 
=== Room CHS 16-154 ===

Latest revision as of 18:19, 14 March 2014

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

Main course page for Principles of Neuroimaging (2012-13)
M284A Principles of Neuroimaging A

Week 1 - A late start

Monday 1/6/14, Wednesday 1/8/14 - No Class

Week 2 - in class lab project

Monday 1/13/14, Wednesday 1/15/14

- EKG Circuit Build. Speaker: Cameron Rodriguez

Week 3 - Swine flu and MRI

Monday 1/20/14

Class canceled due to flu. Sorry

Wednesday 1/22/14

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

OUTLINE Required Readings

HahnFig1.png above: Figure 1 from Hahn, 1950

Suggested Further Reading

File:PSatSeq.jpg

Week 4 - Magnetic Resonance Imaging

Monday 1/27/1 - MRI

-MRI I Speaker: Cohen

Required Readings

Wednesday 1/29/14 - MRI II. Speaker: Cohen

Week 5 MRI and multimodal imaging

Monday 2/3/14

MRI (fMRI) III. Speaker: Cohen

Wednesday 2/5/14

Multimodal imaging. Speaker: Cohen

Week 6 Diffusion and PET

Monday 2/10/14

Diffusion imaging. 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 2/12/14

Positron Emission Tomography. Speaker: Magnus Dahlboun

Handouts distributed in class.

Week 7

Monday 2/17/14 Presidents Day - No class

Wednesday 2/19/14

Week 8 Transcranial Magnetostimulation and PET applications

Monday 2/24/14

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 2/26/1.

PET applications. Speaker: Edythe London

Week 9 - Spectroscopy

Monday 3/3/14 - Class canceled

Wednesday 3/5/14

Spectroscopy. Speaker: Albert Thomas

Handouts distributed in class

Week 10 - Compressed sensing and finals

Monday 3/10/14

Compressed Sensing. Speaker: Ming Yan

To access the slides from the course web site listed on his handout, The username is "caame654", and password is "dense".

Suggested Further Reading

  • READING
"An Introduction to Compressive Sampling" EJ Candes, MB Watkin, IEEE Signal Processing Magazine, March, 2008 <-- Mark's favorite. This is a good overview of the field.
"Sparse MRI: The Application of Compressed Sensing for Rapid MR Imaging" M. Lustig, D. Donoho, J.M. Pauly, Magn. Reson. Med 58:1182–1195, 2007 Lustig demonstrates each step in the process with examples using MRI.
"Compressed Sensing", D. Donoho, IEEE Trans. Inform. Theory 52:1289, 2006 One of the more accessible formal discussions of CS
Rice University Compressed Sensing Resources. A repository of scholarly work on CS.
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