Principles of Neuroimaging B - 2011: Difference between revisions
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=Lecture Videos= | =Lecture Videos= | ||
*[[Media:1_3_11_mark_cohen_mri.mp4| | *[[Media:1_3_11_mark_cohen_mri.mp4|Friday 1-3-11 - MR Signals and Contrast, Speaker Mark Cohen]] | ||
*[[Media:1_5_11_mark_cohen_mri_p1.mp4|Wednesday 1-5-11 - MR Spatial Encoding I, Speaker Mark Cohen]] | *[[Media:1_5_11_mark_cohen_mri_p1.mp4|Wednesday 1-5-11 - MR Spatial Encoding I, Speaker Mark Cohen]] | ||
*[[Media:1_5_11_mark_cohen_mri_p2.mov|Wednesday 1-5-11 - MR Spatial Encoding II, Speaker Mark Cohen]] | *[[Media:1_5_11_mark_cohen_mri_p2.mov|Wednesday 1-5-11 - MR Spatial Encoding II, Speaker Mark Cohen]] | ||
*[[Media:1_10_11_mark_cohen_mri.mp4| | *[[Media:1_10_11_mark_cohen_mri.mp4|Friday 1-10-11 - fMRI and Diffusion, Speaker Mark Cohen]] | ||
*[[Media:1_12_11_mark_cohen_mri.mp4|Wednesday 1-12-11 - fMRI Image Quality and Artifacts, Speaker Mark Cohen]] | *[[Media:1_12_11_mark_cohen_mri.mp4|Wednesday 1-12-11 - fMRI Image Quality and Artifacts, Speaker Mark Cohen]] | ||
*[[Media:1_24_11_susan_bookheimer_exp_design_p1.mp4| | *[[Media:1_24_11_susan_bookheimer_exp_design_p1.mp4|Friday 1-24-11 - Experimental Design I, Speaker Susan Bookheimer]] | ||
*[[Media:1_24_11_susan_bookheimer_exp_design_p2.mov| | *[[Media:1_24_11_susan_bookheimer_exp_design_p2.mov|Friday 1-24-11 - Experimental Design II, Speaker Susan Bookheimer]] | ||
*[[Media:1_26_11_nathan_hageman_dti.mp4|Wednesday 1-26-11 - DTI, Speaker Nathan Hageman]] | *[[Media:1_26_11_nathan_hageman_dti.mp4|Wednesday 1-26-11 - DTI, Speaker Nathan Hageman]] | ||
*[[Media:1_31_11_gregory_simpson_meg_eeg.mp4|Friday 1-31-11 - MEG/EEG, Speaker Gregory Simpson]] | |||
*[[Media:2_2_11_low_field_mri.mp4|Wednesday 2-2-11 - Ultra Low Field MRI, Speaker Konstantin Penanen]] | |||
*[[Media:2_9_11_allan_wu_tms.mp4|Wednesday 2-9-11 - TMS, Speaker Allan Wu]] | |||
*[[Media:2_14_11_jeff_algers_mrs.mp4|Friday 2-14-11 - MRS, Speaker Jeff Algers]] | |||
=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 | ||
==''Wednesday 1/4/12'' - MRI. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]== | |||
OUTLINE | |||
''Required Readings'' | ''Required Readings'' | ||
:*[[media:MRIforPNIB.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 | ||
| Line 31: | Line 36: | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
: | [[image:PSatSeq.jpg|right]] | ||
=='' | |||
==''Friday 1/6/12'' - MRI II. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]== | |||
OUTLINE | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
:*[[media:MRIforPNIB.pdf | MRI Slides (same as 1/4/12)]] | |||
''Suggested Further Reading'' | |||
:*READING | :*READING | ||
:*[[Media:PS1-PNIB2011.pdf | Problem Set 1]] | |||
:* | |||
WEEKLY SUMMARY | |||
=Week 2 MRI Applications= | |||
=='' | ==''Wednesday 1/11/12'' - Diffusion. ''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'' | ||
:* | :* | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:*READING | :*READING | ||
=='' | |||
==''Friday 1/13/12'' - 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/ | :*[http://www.brainmapping.org/NITP/PNA/Readings/MRIforNITP.pdf slides (same as 1/3/12)] | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:*READING | :*READING | ||
=Week 3 Advanced MRI Sequences= | =Week 3 Advanced MRI Applications and Sequences= | ||
=='' | ==''Wednesday 1/18/12'' - Connectivity. ''Speaker'': | ||
'' | [http://ccn.ucla.edu/~jbrown/ Jesse Brown]== | ||
OUTLINE | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
| Line 76: | Line 82: | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:*[http://www. | :*[[Media:DTIHageman.pdf | Hageman DTI Slides]] | ||
:*[http://www. | :*[[Media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]] | ||
:*[http://www. | :*[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] | |||
=Week 4 Applied fMRI, Diffusion Tractography= | =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. | 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. | ||
=='' | ==''Friday 1/24/12'' - Experimental Design. ''Speaker'': [http://www.brainmapping.org/SusanBooheimer Susan Bookheimer]== | ||
OUTLINE | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
| Line 93: | Line 103: | ||
:*[[media:ExperimentalDesign-1-SB.pdf | Experimental Design lecture slides (2010)]] | :*[[media:ExperimentalDesign-1-SB.pdf | Experimental Design lecture slides (2010)]] | ||
==''Wednesday 1/26/ | ==''Wednesday 1/26/12'' - 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]] | [[image:DSIClusteringTwo.jpg|right]] | ||
OUTLINE | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
=Week 5 MEG, EEG, Low Field MRI= | =Week 5 MEG, EEG, Low Field MRI= | ||
| Line 112: | Line 113: | ||
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. | ||
=='' | ==''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] | [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] | ||
| Line 119: | Line 120: | ||
[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.] | [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 | OUTLINE | ||
[[image:miniscanGB.jpg|right]] | [[image:miniscanGB.jpg|right]] | ||
| Line 139: | Line 140: | ||
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. | ||
=='' | ==''Friday 2/7/12'' - Positron Emission Tomography (PET). ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlbom]== | ||
OUTLINE | OUTLINE | ||
[[image:ParallaxError.jpg|right]] | [[image:ParallaxError.jpg|right]] | ||
| Line 148: | Line 149: | ||
:*READING | :*READING | ||
==''Wednesday 2/9/ | ==''Wednesday 2/9/12'' - Transcranial Magneto Stimulation (TMS). ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]== | ||
'Required Readings'' | 'Required Readings'' | ||
:* [[media: | :* [[media:TMS_Wu_2011.pdf | Wu 2011 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: | ||
| Line 161: | Line 164: | ||
=Week 7 Spectroscopy and PET= | =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. | 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 | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
| Line 167: | Line 170: | ||
''Suggested Further Reading'' | ''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: | ||
==''Wednesday 2/16/ | |||
:*[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.] | |||
==''Wednesday 2/16/12''- 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]] | ||
:* [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'' | ''Suggested Further Reading'' | ||
:* | :*n/a | ||
=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. | ||
=='' | ==''Friday 2/21/12'' - Presidents Day.== | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:*[http://en.wikipedia.org/wiki/George_Washington George Washington] | :*[http://en.wikipedia.org/wiki/George_Washington George Washington] | ||
:*[http://en.wikipedia.org/wiki/Abraham_Lincoln Abraham Lincoln] | :*[http://en.wikipedia.org/wiki/Abraham_Lincoln Abraham Lincoln] | ||
==''Wednesday 2/23/ | ==''Wednesday 2/23/12'' - PCA, ICA, Machine learning. ''Speaker'': [http://www.stat.ucla.edu/~yuille/index.html Alan Yuille]== | ||
OUTLINE | OUTLINE | ||
[[image:Probmodel.jpg|right]] | [[image:Probmodel.jpg|right]] | ||
| Line 194: | Line 203: | ||
=Week 9 Functional Connectivity, Multimodal Integration= | =Week 9 Functional Connectivity, Multimodal Integration= | ||
WEEKLYSUMMARY | WEEKLYSUMMARY | ||
=='' | ==''Friday 2/28/12'' - Functional Connectivity. ''Speaker'': [http://alenarto.bol.ucla.edu/ Agatha Lenartowicz]== | ||
OUTLINE | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
:* | :*[[media:functionalconnectivity.pdf | Functional Connectivity Lecture Slides]] | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:* | |||
==''Wednesday 3/2/ | 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 | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
:* | :*[[media:MultiModalNITP2012SM.pdf | Lecture Slides for 3-2-11]] | ||
=Week 10 tbd= | =Week 10 tbd= | ||
This week is presently left open for added topics and makeup as needed. | This week is presently left open for added topics and makeup as needed. | ||
=='' | ==''Friday 3/7/12'' - Final Distributed. ''MSC''== | ||
OUTLINE | OUTLINE | ||
''Required Readings'' | ''Required Readings'' | ||
| Line 217: | Line 235: | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:*READING | :*READING | ||
==''Wednesday 3/9/ | |||
==''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'' | ''Required Readings'' | ||
:* | :*[[media:AndrewsAM_Part1_09Mar2011.pdf | Andrews Lecture Slides]] | ||
:*[[media:PWeissNITP2011.pdf | Weiss Lecture Slides]] | |||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
:*READING | :*READING | ||
=Finals Week= | =Finals Week= | ||
Latest revision as of 03:41, 16 January 2014
Principles of Neuroimaging B, Winter, 2010 - 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 1/4/12 - 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 1/6/12 - MRI II. Speaker: Cohen
OUTLINE Required Readings
Suggested Further Reading
- READING
WEEKLY SUMMARY
Week 2 MRI Applications
Wednesday 1/11/12 - Diffusion. Speaker: Jeffry Alger
OUTLINE
Required Readings
Suggested Further Reading
- READING
==Friday 1/13/12 - fMRI. Speaker:
Cohen==
OUTLINE
Required Readings
Suggested Further Reading
- READING
Week 3 Advanced MRI Applications and Sequences
==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):
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.
Friday 1/24/12 - Experimental Design. Speaker: Susan Bookheimer
OUTLINE Required Readings
Suggested Further Reading
Wednesday 1/26/12 - Tractography using MRI Diffusion. Speaker: Nathan Hageman
OUTLINE Required Readings
Week 5 MEG, EEG, Low Field MRI
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.
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.
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
'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 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:
Wednesday 2/16/12- Positron Emission Tomography (PET) Applications. Speaker: Edythe London
OUTLINE
Required Readings
Suggested Further Reading
- n/a
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