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=NOTICE 5-18-09=
You will find videos, as they become available, at [http://www.brainmapping.org/NITP/PNIvideo.html http://www.brainmapping.org/NITP/PNIvideo.html].

=General=
In Spring Quarter, M285 (Functional MRI) and M284B (Principles of Neuroimaging B) will be taught concurrently. M285 is offered Monday/Wednesday from 2:00 pm to 3:30 for 3 units of credit. Principles of Neuroimaging is offered for 4 units Monday/Wednesday/Friday from 2:00 pm to 3:30 p.m.

We will meet in three different rooms for the quarter:
* '''Mondays''' 2-3:30p Room C8-885 on the C floor of the NPI building
* '''Wednesdays''' Marisa Leif Conference room, 300 Medical Plaza, 3d floor
* '''Fridays''' (''M284B'') Room C8-872 on the C floor of the NPI building

A PTE number is required in order to enroll for M285 on URSA. You can obtain a number by coming to class on the first day, or by contacting [mailto:mscohen@ucla.edu Mark Cohen]. It would be helpful if the word "M285" or "M284" appears in the subject line of your email.

:Prerequisites:
::'''Functional MRI''' - ''Statistics'': Descriptive statistics, hypothesis testing
::'''Principles of Neuroimaging B''' - [http://ccn.ucla.edu/wiki/index.php/Principles_of_Neuroimaging M284A] is required for credit

Students who feel that they need more background in Statistics before beginning are recommended to read:
:[http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025 The Cartoon Guide to Statistics - Gonick $17.95 new]
:The latter teaches stats at what I feel to be the right level - developing intuitions about the kinds of questions that can be answered using stats and about the statistical tests and measures
:[http://www.statsoft.com/textbook/stbasic.html Statsoft online text (''free'')] is another excellent resource

==Objectives==
''284B''. '''Principles of Neuroimaging II'''. (4) Lecture, four hours. Preparation: competence in integral calculus, electricity and magnetism, computer programming (any language), general statistics. Requisite: course 292 and 284A. Instrumental imaging methods for study of nervous system, with emphasis on quantitative understanding and data interpretation and features common to modalities. X-ray computed tomography, magnetic resonance imaging, positron emission tomography, magnetoencephalography, transcranial magneto stimulation, near infrared imaging. Letter grading.

''M285''. '''Functional Neuroimaging''': ''Techniques and Applications''. (3) (Same as Biomedical Physics M285.) Lecture, three hours. In-depth examination of activation imaging, including MRI and electrophysiological methods, data acquisition and analysis, experimental design, and results obtained thus far in human systems. Strong focus on understanding technologies, how to design activation imaging paradigms, and how to interpret results. Laboratory visits and design and implementation of functional MRI experiment. S/U or letter grading.

==Course Overlap==
The Friday lectures for Principles of Neuroimaging B are open to all students, but will typically assume knowledge of mathematics, engineering, electronics and programming.

Receiving a Certificate of Training in the NeuroImaging Training program requires at least two quarters of the fMRI journal club (but we really appreciate continuous attendance) in addition to completion of Principles of Neuromaging, parts A and B

=Schedule=
===Week 1: ===
'''Mon 3/30/09'''
::Neurovascular Coupling - [mailto:sbook@ucla.edu ''Susan Bookheimer'']
[[media:NVcoupling.pdf|Neurovascular coupling, Overview of fMRI and PET Data Acquisition.pdf]]

'''Wed 4/1/09'''
::Overview of fMRI - [mailto:sbook@ucla.edu ''Susan Bookheimer'']

'''Fri 4/3/09'''
::PET Data Acquisition - [mailto::MDahlbom@mednet.ucla.edu ''Magnus Dahlbom'']

===Week 2: ===
'''Mon 4/6/09'''
::Experimental Design I - [mailto:sbook@ucla.edu ''Susan Bookheimer'']
[[media:ExperimentalDesign-1-SB.pdf|ExperimentalDesign-1-SB.pdf]]

'''Wed 4/8/09'''
::Experimental Design II - [mailto:sbook@ucla.edu ''Susan Bookheimer'']
[[media:ExperimentalDesign-2.pdf|ExperimentalDesign-2-SB.pdf]]

'''Fri 4/10/09'''
::''NO CLASS TODAY''

===Week 3: ===
'''Mon 4/13/09'''
''READINGS:''

A PDF of all of the slides used of for this week can be found here: [http://www.brainmapping.org/NITP/PNB/MRIforNITP2009.pdf MRI for NITP]

I had promised a reading on the Fourier transform math: [[Media:Mathematical_tools.pdf | Mathematical Tools]]

''Here are some additional readings on MRI, for those who felt that I was covering the material too fast''
:[http://airto.hosted.ats.ucla.edu/BMCweb/CourseWork/M285/MRI/RMWFundamentals.html Physical Foundations of MR imaging]
:[http://airto.hosted.ats.ucla.edu/BMCweb/CourseWork/M285/MRI/MRBasics.html General Principles of Image Contrast]
:[http://www.cis.rit.edu/htbooks/mri/ (my favorite:) The Basics of MRI, an online programmed textbook]

::Magnetic Resonance Imaging I - [mailto:mscohen@ucla.edu ''Mark Cohen'']
:::''Signals and Contrast''

'''Wed 4/15/09'''
::Magnetic Resonance Imaging - [mailto:mscohen@ucla.edu ''Mark Cohen'']
:::''Imagers and Sequences''

'''Fri 4/17/09'''
::Advanced Topics in MRI - [mailto:mscohen@ucla.edu ''Mark Cohen'']
:::''Instrumentation''

===Week 4: ===
'''Todays's meeting is in Room 78-215'''

'''Mon 4/20/09'''
::Understanding Artifacts in MRI and fMRI - [mailto:mscohen@ucla.edu ''Mark Cohen'']

'''Wed 4/22/09'''
::Pre-Processing - [mailto:poldrack@ucla.edu ''Russ Poldrack'']
[http://ccn.ucla.edu/wiki/index.php/Image:Preprocessing.pdf Preprocessing slides]

'''Fri 4/24/09'''
::Optical Intrinsic imaging [http://www.loni.ucla.edu/About_Loni/people/Indiv_Detail.jsp?people_id=264 KC Brennan]

===Week 5: ===
'''Mon 4/27/09'''
::Registration and Normalization - [mailto:poldrack@ucla.edu ''Russ Poldrack'']
[http://ccn.ucla.edu/wiki/images/a/a1/SpatialTransformation.pdf Spatial registration slides]

'''Wed 4/29/09'''
::Computational Anatomy - [mailto:esowell@ucla.edu ''Elizabeth Sowell'']

'''Fri 5/1/09'''
::Diffusion and its Effects on MR Signal - [mailto:mscohen@ucla.edu ''Mark Cohen'']

===Week 6: ===
'''Mon 5/4/09'''
::Diffusion Tensor Imaging and Tractography - TBD

'''Wed 5/6/09'''
::Linearity of the fMRI signal - [mailto:mscohen@ucla.edu ''Mark Cohen'']
::First Level Statistics of fMRI images - [mailto:jeanette.mumford@gmail.com ''Jeanette Mumford (unconfirmed)'']
'''Fri 5/8/09'''
::Whitening/Coloring, Autocorrelation, Power - [mailto:jeanette.mumford@gmail.com ''Jeanette Mumford (unconfirmed)'']
[http://www.brainmapping.org/NITP/Mumford5-8-09.mov Lecture video]

===Week 7: ===
'''Mon 5/11/09'''
::Massively Univariate Stats, Group Analysis- [mailto:jeanette.mumford@gmail.com ''Jeanette Mumford (unconfirmed)'']
[http://www.brainmapping.org/NITP/Mumford5-11-09.mov Lecture video]

'''Wed 5/13/09'''
::Multiple comparisons - [mailto:jeanette.mumford@gmail.com ''Jeanette Mumford'']

[http://www.brainmapping.org/NITP/Mumford5-13-09.mov9 Lecture video]
'''Fri 5/15/09'''
::no class

===Week 8: ===
'''Mon 5/18/09'''
::ROI-based Analyses - [mailto:sbook@ucla.edu ''Susan Bookheimer'']

[http://www.brainmapping.org/NITP/Bookheimer5-18-09.mov Lecture video]

'''Wed 5/20/09'''
::Multimodal Analysis - [mailto:mscohen@ucla.edu ''Mark Cohen'']

[http://ccn.ucla.edu/wiki/images/3/39/MultiModalM285.pdf Multimodal Imaging slides]

'''Fri 5/22/09'''
::Multimodal Data Collection, Integration of MRI and EEG data - Special Lecture: Robin Goldman, Columbia University

===Week 9: ===
'''Mon 5/25/09''' is Memorial Day. ''No Class''

'''Wed 5/27/09'''
::Connectivity - [mailto:poldrack@ucla.edu ''Russ Poldrack'']

[http://ccn.ucla.edu/wiki/images/c/c0/Connectivity.pdf Slides]

'''Fri 5/29/09'''
::Special Lecture: Allan Wu, TMS

[http://ccn.ucla.edu/wiki/images/4/4a/TMS-05-28-09-handout.pdf TMS slides]

===Week 10: ===
'''Mon 6/1/09'''
::Reporting fMRI data, Reverse Inference - [mailto:poldrack@ucla.edu ''Russ Poldrack'']

[http://ccn.ucla.edu/wiki/images/8/83/ReportingfMRIData.key.pdf Slides]

'''Wed 6/3/09'''
::Special Populations - [mailto:sbook@ucla.edu ''Susan Bookheimer'']

'''Fri 6/5/09'''
::NITP / Principles of Neuroimaging Class Party and Certificates
:::''Sorry - Attendance limited...''

===Finals Week===

Principles of Neuroimaging B / functional MRI - Revision history

Ccn admin: 1 revision

Elau: Undo revision 2716 by Aenalb (talk)