Course Cancelled

Spring 2008

Brain Imaging Laboratory

fMRI Data Acquisition and Analysis in Cognitive Neuroscience

Graduate Class 2476 Class Number 33832 Undergraduate Class PSY 1054 Class Number 32813.

Meeting times Lecture Monday Wednesday 300 4:30-5:45 EH, Lab Friday 303 1-5 PM EH

Instructor Walter Schneider, Course Director (wws@pitt.edu, 629 LRDC)

Teaching Assistant (yet to be assigned)

Course Goal: To provide you operational laboratory skills for fMRI research in Pittsburgh.

Announcements

This course was cancelled for Spring 2008 it may be offered Spring 2009

This is a course in which you will learn brain imaging research skills. It will provide both MRI time and training to do a pilot study. Students will be able to do pilot research projects. .

Sample Image gallery illustrating methods covered in the course (click to enlarge)

Course Abstract

This course provides students an understanding of cognitive neuroscience use of brain imaging and the skills to create, analyze, and interpret fMRI (functional Magnetic Imaging This course provides students an understanding of cognitive neuroscience use of brain imaging and the skills to create, analyze, and interpret fMRI (functional Magnetic Imaging Research) brain imaging research. This is a laboratory course with the goal to teach practical skills and techniques to program, run, analyze and write up an fMRI experiments. This course will provide an opportunity for students to design an fMRI experiment, to acquire pilot data, and to analyze the data. Students will learn to use tools to compute image pre-processing (e.g., effects of different registration and normalization procedures) and data analysis (e.g., the use of GLM-based techniques for fast event-related designs, approaches to investigating functional interconnectivity, and tracking cortical connections). We anticipate that students will complete the semester with pilot data and a functional paradigm. If run to completion we would expect the work to be of publication quality. Students will likely have an opportunity to apply for additional imaging hours to extend their pilot project. This will be a laboratory course. We will meet in a computer room for labs to learn to use professional research tools. We will describe and use multiple packages, many exercises will be utilize BrainVoyager QX and other tools such as FSL SPM, and AFNI. There will be two lectures (1.25 hr) and one (2-4 hr) lab per week. Prerequisites: courses in statistical methods and upper level psychology, cognitive neuroscience, or bioengineering course. The course is available to graduate students, advanced undergraduates, and postdoctoral students.

Undergraduate Students Cross Listing.

Advanced undergraduates will find this course provides a great entry into brain imaging research. It is an opportunity for learning advanced cognitive neuroscience research skills. The methods could be the basis for an undergraduate thesis. The skills learned in the course have allowed students to gain laboratory assistant jobs locally and nationally doing research in the exciting field of brain imaging. Undergraduates do the readings and exams as do the graduate students. In the research project effort, criterion for knowledge of the literature and research program design are graded on a separate scale than the graduate students. Students should be comfortable with working with computers and statistical analysis. Email Walter Schneider (wws@pitt.edu) with questions an permission requests.

Auditors, Visitors Post-docs, faculty.

Visitors are welcome to attend the lectures. Space in the labs is limited to 25 computer stations with priority to those registered in the course. The priority for access is registered students, auditors, then visitors. Auditors need not take the exams or do a research project. Visitors should send an email note to the TA indicating what labs they wish to attend. If you would like to receive an email about fMRI teaching events send you can sign to the distribution list. The classes are in Engineering Hall on the Pitt campus next to LRDC

Lectures. Note as lectures are given links will be activated to get notes from the lectures.

This is a DRAFT syllabus and will be updated as the course proceeds. The content is expected to closely follow (90% match) the details shown below. The Lecture Links below are based on the lectures given in Spring 2006. They will be updated before they are presented.

Reading links require enter the login and password of brain click on the lecture or readings to download.

Tentative Lecture Topics fMRI Lab Psy 2476 Class 18528
#	Date	Day	Topic	Readings # indicates Chapter
1	7-Jan	Wed	1)       Introduction and course overview	HSM #1, Savoy 2002
2	9-Jan	Mon	2)       E-Prime programming basics conceptualization of experiment	E-Prime UG #2
3	14-Jan	Wed	3)       E-Prime code programming experiments	E-Prime UG #3, UG #4
4	16-Jan	Mon	ML King day - No Class
5	21-Jan	Wed	4) Specialized use of E-Prime, Basics Timing	Handout fMRI & E-Prime
6	23-Jan	Mon	5)       E-Prime fMRI synchronization, time audit and running in magnet
7	28-Jan	Wed	6)       Overview of fMRI paradigm deign and analysis methods	HSM # 10, BV GSG 1-38
8	30-Jan	Mon	7)       fMRI data processing, Introduction to Brain Voyager – Preprocessing	BV GSG 39-64
9	4-Feb	Wed	8)    Spatial normalization – alignment in Talairach, Cross reference to atlases Review of cortical anatomy and cortical systems	Brain Tutor Handout, Attention, exec sys, affect memory
10	6-Feb	Mon	9)       fMRI General Linear Model (GLM)	HSM #12 BV User Guide 65-70
11	11-Feb	Wed	11)   Experimental design block, slow event, fast event, mixed; Threshold for significance correction & False Discovery Rate fMRI, Example of new design projects, making an experiment have impact, library research link (No lecture Notes free discussion) Power Point presentation Template, Example N-Nback; Endnote Library of fMRI (references 20meg)	Nelsen 2005, Genovese et al. 2002, HSM #11, Chein & Schneider 2002;
12	13-Feb	Mon	12)       Safety & Ethics in fMRI experiments, ethics (REQIURED CLASS if you will be scanning	Illes et al 2004,Katzman, 1999, Illes 2006, Hilgenberg 2006, Illes 2005
13	18-Feb	Wed	13)    Design continued and statistical power, Power Spreadsheet	Desmond 2002, Murphy 2004;
14	20-Feb	Mon	14)   (continuation of previous)
15	25-Feb	Wed	15)     Practical guide to subject running, IRB, Screening form,	BV documentation
16	27-Feb	Mon	16) Convolution analysis methods (Delayed till after break) M. Cole	Dale 97, Burdock 98, Serences, 2004; optional Dale 99
17	3-Mar	Wed	17)    Strategy of fMRI research projects	Starter 1996;Kanwisher 1997; 2001; Haxby 2001; Spector Kanwisher 2004
18	5-Mar	Mon	18) Writing up an fMRI experiment	Sample Paper Chein & Schneider 2005; Journal Impact Factors
19	10-Mar	Wed	Spring Break
20	12-Mar	Mon	Spring Break
21	17-Mar	Wed	19)    Statistical power in fMRI designs	(being updated)
22	19-Mar	Mon	20)    Learning/using multiple fMRI Paths SPM, AFNI, FSL	(being updated)
23	24-Mar	Wed	21)    Presentation of design proposals for student projects	(being updated)
24	26-Mar	Mon	22)    Spatial normalization Flat mapping, ROI alignment, sphere alignment	(being updated)
25	31-Mar	Wed	23)    Correlation across subjects and free viewing experiments, Virtual Reality assessment part 2	(being updated)
26	2-Apr	Mon	24)    Establishing causal relationships – Dynamic Causal Modeling, Granger Causality	(being updated)
27	7-Apr	Wed	25)    Data Mining techniques	(being updated)
28	9-Apr	Mon	26)    Fiber tracing using Diffusion Tensor imaging	(being updated)
29	14-Apr	Wed	27)    Advanced intro – real time imaging, EEG source localization, other	(being updated)
30	16-Apr	Mon	28)    Presentation of student projects
31	18-Apr	Wed	29)    FINAL

Laboratory

The main goal of the course is mastery of the skills to do successfully fMRI experiments. There are many scientific and procedural skills that must be mastered to do successful fMRI research. The laboratory provides detailed experience of performing the needed operations.

Labs	Topic
11-Jan	Lab procedures, installation of E-Prime, discussion of projects
18-Jan	E-Prime basics and code
25-Jan	E-Prime fMRi methods