Principles of Neuroimaging B - 2011: Difference between revisions

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=Principles of Neuroimaging B, Winter, 2010 - Class Schedule and Syllabus=
=Principles of Neuroimaging B, Winter, 2010 - Class Schedule and Syllabus=
:'''[[Principles_of_Neuroimaging_-_2010-2011 | Main course page for Principles of Neuroimaging (2010-11)]]'''
:'''[[Principles_of_Neuroimaging_-_2010-2011 | Main course page for Principles of Neuroimaging (2010-11)]]'''
:'''[[Principles_of_Neuroimaging_A_-_2010 | M284A Principles of Neuroimaging A]]'''
:'''[[Principles_of_Neuroimaging_A_-_2010 | M284A Principles of Neuroimaging A]]'''


=Week 1 Magnetic Resonance Imaging=
=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
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.
[[image:PSatSeq.jpg|right]]
==''Monday 1/3/11'' - MR Signals and Contrast. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]==
==''Monday 1/3/11'' - MR Signals and Contrast. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]==
I will be speaking from [http://www.brainmapping.org/NITP/PNA/Readings/MRIforNITP.pdf these slides]
I will be speaking from [http://www.brainmapping.org/NITP/PNA/Readings/MRIforNITP.pdf these slides]
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''Suggested Further Reading''
''Suggested Further Reading''
:*This week we concern ourselves with nitty-gritty issues in MRI and with the important application of functional MRI.
:*This week we concern ourselves with nitty-gritty issues in MRI and with the important application of functional MRI.
=Week 2 Practical MRI=
=Week 2 Practical MRI=
WEEKLYSUMMARY
WEEKLYSUMMARY
==''Monday 1/10/11'' - MRI Artifacts & fMRI. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]==
==''Monday 1/10/11'' - MRI Artifacts & fMRI. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]==
OUTLINE
OUTLINE
[[image:Bandwidth.jpg|right]]
''Required Readings''
''Required Readings''
:*[http://www.brainmapping.org/NITP/PNA/Readings/MRIforNITP.pdf slides (same as 1/3/11)]
:*[http://www.brainmapping.org/NITP/PNA/Readings/MRIforNITP.pdf slides (same as 1/3/11)]
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''Suggested Further Reading''
''Suggested Further Reading''
:*READING
:*READING
==''Wednesday 1/12/11'' - fMRI. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]==
==''Wednesday 1/12/11'' - fMRI. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]==
OUTLINE
OUTLINE
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OUTLINE
OUTLINE
''Required Readings''
''Required Readings''
:*READING
:*[[media:ExperimentalDesign-1-SB.pdf | Experimental Design lecture slides]]


''Suggested Further Reading''
''Suggested Further Reading''
:*READING
:*[[media:ExperimentalDesign-1.pdf | Russ Poldrack experimental design lecture (part 1)]]
:*[[media:ExperimentalDesign-2.pdf | Russ Poldrack experimental design lecture (part 2)]]
:*[[media:DesignLecture.pdf | Experimental design lecture]]
 
==''Wednesday 1/26/11'' - Tractography using MRI Diffusion. ''Speaker'': [http://www.loni.ucla.edu/About_Loni/people/Indiv_Detail.jsp?people_id=183 Nathan Hageman]==
==''Wednesday 1/26/11'' - Tractography using MRI Diffusion. ''Speaker'': [http://www.loni.ucla.edu/About_Loni/people/Indiv_Detail.jsp?people_id=183 Nathan Hageman]==
[[image:DSIClusteringTwo.jpg|right]]
OUTLINE
OUTLINE
''Required Readings''
''Required Readings''
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''Suggested Further Reading''
''Suggested Further Reading''
:*READING
:*READING
=Week 5 MEG, EEG, Low Field MRI=
=Week 5 MEG, EEG, Low Field MRI=
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.
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.
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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


==''Monday 1/31//11'' - Ultralow field MRI. ''Speaker'': ''Konstantin Penanen'' NASA/CalTech Jet Propulsion Laboratory==
==''Monday 1/31//11'' - Ultralow field MRI. ''Speaker'': '''Konstantin Penanen''' NASA/CalTech Jet Propulsion Laboratory (''unconfirmed'')==
OUTLINE
OUTLINE
[[image:miniscanGB.jpg|right]]
''Required Readings''
''Required Readings''
:*READING
:*READING
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''Suggested Further Reading''
''Suggested Further Reading''
:*READING
:*READING
==''Wednesday 2/2/11'' - MEG and EEG. ''Speaker'': [http://www.labome.org/expert/usa/university/simpson/gregory-v-simpson-1030707.html Greg Simpson ''unconfirmed'']==
==''Wednesday 2/2/11'' - MEG and EEG. ''Speaker'': [http://www.labome.org/expert/usa/university/simpson/gregory-v-simpson-1030707.html Greg Simpson ''unconfirmed'']==
[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]
[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]
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==''Monday 2/7/11'' - Positron Emmission Tomography (PET) Applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]==
==''Monday 2/7/11'' - Positron Emmission Tomography (PET) Applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]==
OUTLINE
OUTLINE
[[image:SmokerStroop.png|right]]
''Required Readings''
''Required Readings''
:*READING
:*READING
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''Suggested Further Reading''
''Suggested Further Reading''
:*READING
:*READING
==''Wednesday 2/9/11'' - Transcranial Magneto Stimulation (TMS). ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]==
==''Wednesday 2/9/11'' - Transcranial Magneto Stimulation (TMS). ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]==
OUTLINE
OUTLINE
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==''Wednesday 2/16/11'' - Positron Emission Tomography (PET) Applications. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlbom]==
==''Wednesday 2/16/11'' - Positron Emission Tomography (PET) Applications. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlbom]==
OUTLINE
OUTLINE
[[image:ParallaxError.jpg|right]]
''Required Readings''
''Required Readings''
:*[[media:PET_2010.pdf | PET Imaging handout]]
:*[[media:PET_2010.pdf | PET Imaging handout]]
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''Suggested Further Reading''
''Suggested Further Reading''
:*READING
:*READING
=Week 8 Machine Learning=
=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.
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.
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==''Wednesday 2/23/11'' - PCA, ICA, Machine learning. ''Speaker'': [http://www.stat.ucla.edu/~yuille/index.html Alan Yuille]==
==''Wednesday 2/23/11'' - PCA, ICA, Machine learning. ''Speaker'': [http://www.stat.ucla.edu/~yuille/index.html Alan Yuille]==
OUTLINE
OUTLINE
[[image:Probmodel.jpg|right]]
''Required Readings''
''Required Readings''
:*READING
:*READING
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''Suggested Further Reading''
''Suggested Further Reading''
:*READING
:*READING
=Week 9 Functional Connectivity, Multimodal Integration=
=Week 9 Functional Connectivity, Multimodal Integration=
WEEKLYSUMMARY
WEEKLYSUMMARY

Revision as of 15:54, 26 September 2010

Principles of Neuroimaging B, Winter, 2010 - Class Schedule and Syllabus

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

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.

File:PSatSeq.jpg

Monday 1/3/11 - MR Signals and Contrast. Speaker: Cohen

I will be speaking from these slides

Required Readings

HahnFig1.png above: Figure 1 from Hahn, 1950

Suggested Further Reading

  • READING

Wednesday 1/5/11 - MRI. Speaker: Daniel Ennis

OUTLINE Required Readings

  • READING

Suggested Further Reading

  • This week we concern ourselves with nitty-gritty issues in MRI and with the important application of functional MRI.

Week 2 Practical MRI

WEEKLYSUMMARY

Monday 1/10/11 - MRI Artifacts & fMRI. Speaker: Cohen

OUTLINE

File:Bandwidth.jpg

Required Readings

Suggested Further Reading

  • READING

Wednesday 1/12/11 - fMRI. Speaker: Cohen

OUTLINE Required Readings

Suggested Further Reading

  • READING

Week 3 Advanced MRI Sequences

We are fortunate to feature Jin Hyung Lee, a recently added faculty member at UCLA. Dr. Lee has pioneered many novel technologies and applications of MRI, with special applications to neuroscience.

Monday 1/17/11 - Martin Luther King Holiday.

Suggested Further Reading

Martin Luther King

Wednesday 1/19/11 - Steady state and other advanced sequences. Speaker: Jin Hyung Lee

OUTLINE Required Readings

  • READING

Suggested Further Reading

Week 4 Applied fMRI, Diffusion Tractography

There is enormous subtlety to the design of pyschophysical and psychological studies made more complex by fitting the experiments into the constrained environment of the MR instrument, the limitations of the BOLD signal and the practical problems of time. This week, Dr. Bookheimer will introduce the design of human functional imaging experiments from the point of view of exposing cognitive process using fMRI.

Monday 1/24/11 - Experimental Design. Speaker: Susan Bookheimer

OUTLINE Required Readings

Suggested Further Reading

Wednesday 1/26/11 - Tractography using MRI Diffusion. Speaker: Nathan Hageman

File:DSIClusteringTwo.jpg

OUTLINE Required Readings

Suggested Further Reading

  • READING

Week 5 MEG, EEG, Low Field MRI

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.

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

Monday 1/31//11 - Ultralow field MRI. Speaker: Konstantin Penanen NASA/CalTech Jet Propulsion Laboratory (unconfirmed)

OUTLINE

File:MiniscanGB.jpg

Required Readings

  • READING

Suggested Further Reading

  • READING

Wednesday 2/2/11 - MEG and EEG. Speaker: Greg Simpson unconfirmed

A story

Required Readings

  • READING

Suggested Further Reading

  • READING

Week 6 PET and TMS

Positron Emission Tomography was the first tomographic means available to explore neural activity in humans. Though this use was made much less common with the advent of fMRI, PET has many tricks up its sleeve. In particular, the technology allows incomparable sensitivity in the localization specific molecular species.

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.

Monday 2/7/11 - Positron Emmission Tomography (PET) Applications. Speaker: Edythe London

OUTLINE

File:SmokerStroop.png

Required Readings

  • READING

Suggested Further Reading

  • READING

Wednesday 2/9/11 - Transcranial Magneto Stimulation (TMS). Speaker: Allan Wu

OUTLINE Required Readings

Suggested Further Reading

  • READING

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.

Monday 2/14/11 - Magnetic Resonance Spectroscopy. Speaker: Jeffry Alger

OUTLINE Required Readings

Suggested Further Reading

  • READING

Wednesday 2/16/11 - Positron Emission Tomography (PET) Applications. Speaker: Magnus Dahlbom

OUTLINE

File:ParallaxError.jpg

Required Readings

Suggested Further Reading

  • READING

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.

Monday 2/21/11 - Presidents Day.

Suggested Further Reading

Wednesday 2/23/11 - PCA, ICA, Machine learning. Speaker: Alan Yuille

OUTLINE

File:Probmodel.jpg

Required Readings

  • READING

Suggested Further Reading

  • READING

Week 9 Functional Connectivity, Multimodal Integration

WEEKLYSUMMARY

Monday 2/28/11 - Functional Connectivity. Speaker: Agatha Lenartowicz

OUTLINE Required Readings

  • READING

Suggested Further Reading

  • READING

Wednesday 3/2/11 - Multimodal Integration. Speaker: Cohen

OUTLINE Required Readings

  • READING

Suggested Further Reading

  • READING

Week 10 tbd

This week is presently left open for added topics and makeup as needed.

Monday 3/7/11 - tbd. Speaker: tbd

OUTLINE Required Readings

  • READING

Suggested Further Reading

  • READING

Wednesday 3/9/11 - tbd. Speaker: Cohen

Additional topics and wrapup. Required Readings

  • READING

Suggested Further Reading

  • READING

Finals Week

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