Principles of Neuroimaging B / functional MRI

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NOTICE 5-18-09

You will find videos, as they become available, at


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 Mark Cohen. It would be helpful if the word "M285" or "M284" appears in the subject line of your email.

Functional MRI - Statistics: Descriptive statistics, hypothesis testing
Principles of Neuroimaging B - M284A is required for credit

Students who feel that they need more background in Statistics before beginning are recommended to read:

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
Statsoft online text (free) is another excellent resource


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


Week 1:

Mon 3/30/09

Neurovascular Coupling - Susan Bookheimer

Neurovascular coupling, Overview of fMRI and PET Data Acquisition.pdf

Wed 4/1/09

Overview of fMRI - Susan Bookheimer

Fri 4/3/09

PET Data Acquisition - Magnus Dahlbom

Week 2:

Mon 4/6/09

Experimental Design I - Susan Bookheimer


Wed 4/8/09

Experimental Design II - Susan Bookheimer


Fri 4/10/09


Week 3:

Mon 4/13/09 READINGS:

A PDF of all of the slides used of for this week can be found here: MRI for NITP

I had promised a reading on the Fourier transform math: Mathematical Tools

Here are some additional readings on MRI, for those who felt that I was covering the material too fast

Physical Foundations of MR imaging
General Principles of Image Contrast
(my favorite:) The Basics of MRI, an online programmed textbook
Magnetic Resonance Imaging I - Mark Cohen
Signals and Contrast

Wed 4/15/09

Magnetic Resonance Imaging - Mark Cohen
Imagers and Sequences

Fri 4/17/09

Advanced Topics in MRI - Mark Cohen

Week 4:

Todays's meeting is in Room 78-215

Mon 4/20/09

Understanding Artifacts in MRI and fMRI - Mark Cohen

Wed 4/22/09

Pre-Processing - Russ Poldrack

Preprocessing slides

Fri 4/24/09

Optical Intrinsic imaging KC Brennan

Week 5:

Mon 4/27/09

Registration and Normalization - Russ Poldrack

Spatial registration slides

Wed 4/29/09

Computational Anatomy - Elizabeth Sowell

Fri 5/1/09

Diffusion and its Effects on MR Signal - Mark Cohen

Week 6:

Mon 5/4/09

Diffusion Tensor Imaging and Tractography - TBD

Wed 5/6/09

Linearity of the fMRI signal - Mark Cohen
First Level Statistics of fMRI images - Jeanette Mumford (unconfirmed)

Fri 5/8/09

Whitening/Coloring, Autocorrelation, Power - Jeanette Mumford (unconfirmed)

Lecture video

Week 7:

Mon 5/11/09

Massively Univariate Stats, Group Analysis- Jeanette Mumford (unconfirmed)

Lecture video

Wed 5/13/09

Multiple comparisons - Jeanette Mumford

Lecture video Fri 5/15/09

no class

Week 8:

Mon 5/18/09

ROI-based Analyses - Susan Bookheimer

Lecture video

Wed 5/20/09

Multimodal Analysis - Mark Cohen

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 - Russ Poldrack


Fri 5/29/09

Special Lecture: Allan Wu, TMS

TMS slides

Week 10:

Mon 6/1/09

Reporting fMRI data, Reverse Inference - Russ Poldrack


Wed 6/3/09

Special Populations - Susan Bookheimer

Fri 6/5/09

NITP / Principles of Neuroimaging Class Party and Certificates
Sorry - Attendance limited...

Finals Week