BME 499.098/Biostat 642:
Introduction to Functional MRI

Schedule & Basic Info

Class Meeting Time:	9AM to Noon, Monday-Friday, Aug 12 through Aug 23
Class Meeting place:	East Hall 1068 & 1360; see calendar
Lab Meeting Time:	1PM-3PM
Lab Meeting place:	East Hall B250, PC lab in the basement of East Hall (except as noted)
Instructors:	Luis Hernandez, Tom Nichols, & Doug Noll
Announcements:	If you didn't already, please fill out a Course Evaluation and return it to Eve Gochis in the fMRI lab.

Course Calendar

	Week 1
	Mon 8/12	Tue 8/13	Wed 8/14	Thu 8/15	Fri 8/16
Lecture 9am- Noon	Physics I: NMR, Fields, Gradients (DN) Rm: EH 1068	Physics II: Image formation, SNR, Hardware (DN) Rm: EH 1068	Physics III: BOLD Effect. Artfacts (DN) Rm: EH 1360	Task Design I: Subtraction, Blocked & event-related designs (DN) Rm: EH 1068	Artifacts, image reconstruction, preprocessing (LH) Rm: EH 1360
Lab 1pm- 3pm	Task Design: E' (TW)	Task Design: E' (TW)	fMRI Lab: Safety, tour, scanning. Group A Rm: fMRI Lab	fMRI Lab: Safety, tour, scanning. Group B Rm: fMRI Lab	Matlab intro, Data exploration
	Week 2
	Mon 8/19	Tue 8/20	Wed 8/21	Thu 8/22	Fri 8/23
Lecture 9am- Noon	Stats I: General Linear Model (TN) Rm: EH 1360	Stats II: fMRI Modeling (TN) Rm: EH 1360	Stats III: Multiple comparisons, Group analyses (TN) Rm: EH 1360	Task Design II: Optimizing ER, jitter, nonlinearity (TW) Rm: EH 1360	Presentations, Q & A Rm: EH 1360
Lab 1pm- 3pm	SPM I: Intro, preprocessing (TN/LH)	SPM II: Intrasubject results (TN/LH)	SPM III: Group analyses, project work	Monitored lab time	(none)

Week 1

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Mon Aug 12 Lab: Task Design I
Instructor: Tor Wager
Resources:

Tue Aug 13 Lecture: Physics
Instructor: Doug Noll
See Doug's webpage

Tue Aug 13 Lab: Task Design II
Instructor: Tor Wager
See resources for previous lab

Wed Aug 14 Lecture: Physics
Instructor: Doug Noll
See Doug's webpage

Wed Aug 14 Lab: fMRI Lab Tour (Group A)
Instructor: Luis Hernandez & Doug Noll

Thu Aug 15 Lecture: Task Design I
Instructor: Doug Noll
See Doug's webpage

Thu Aug 15 Lab: fMRI Lab Tour (Group B)
Instructor: Luis Hernandez & Doug Noll

Fri Aug 16 Lecture: Artifacts II
Instructor: Luis Hernandez

Fri Aug 16 Lab: Matlab
Instructor: Tor Wager

Week 2

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Mon Aug 19 Lab: SPM I
Instructor: Tom Nichols & Luis Hernandez
Lab

Tue Aug 20 Lecture: Stats II
Instructor: Tom Nichols

Tue Aug 20 Lab: SPM II
Instructor: Tom Nichols & Luis Hernandez
Lab

Wed Aug 21 Lecture: Stats III
Instructor: Tom Nichols

Wed Aug 21 Lab: SPM III
Instructor: Tom Nichols & Luis Hernandez
Lab

Thu Aug 21 Lecture: Task Design II
Instructor: Tor Wager

Thu Aug 21 Lab: Monitored Lab Time
Instructor: Tom Nichols & Luis Hernandez
You will use this time to work on your project

These files are useful additions to SPM:

• zeronan.m
  This will turn NaN values into zeros. Useful with contrast images before smoothing. Output images have a 'z' prefix.
• spm_orthviews.m
  This is an enhanced orthoviewer. After you are viewing images with 'Dispaly' or 'CheckReg' enter the following command
       spm_orthtviews('addcolorbar')
  You will then get a color bar with each image, and, moreover, you can right click on the color bar to set the max or minimim intensity (hence eliminated multiple spm_orthviews('window'...) calls).

Fri Aug 21 Lecture: Class Presentations!
Instructor: You!

Fri Aug 21 Lab: none

Final Project

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