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Psy 8960(001) fMRI:  Biological Basis and Experimental Design

9:45-11:00 Tuesdays and Thursdays, 203 Elliott Hall

3 credits


In contrast to the version of this course taught Spring ’06, this is a true seminar course.  Student presentations will occupy the bulk of class time.  The syllabus has notes on course organization, a description of the final project and attendance and grading policies. 


Logistics.  The initial class will meet Tuesday, Jan. 16, at 9:45 in 203 Elliott Hall.  Seminar courses usually meet just once a week for a long (3-hour) session - we’ll discuss this possibility, and alternative meeting times, on the first day of class.  To respect the schedules of all attendees, however, an unanimous vote (and room availability) will be required to move the class away from the scheduled time and place. 




Potential Readings (comprehensive list)

Jan 16

BOLD basics


Jan 18


Ogawa ’93. Mini-lecture: Physics 101.

Jan 23

Spin echo:

Parkes ‘05

Jan 25


 . Mini-Lecture:  Echoes and dephasing

Jan 30

BOLD models:

Buxton ’04. Mini-Lecture: Inversion recovery

Feb 1

BOLD variability:

Obata ’05.  Mini-Lecture: QUIPPS II

Feb 6


Lu ’03, Donahue ’06.  Mini-Lecture : VASO

Feb 8


Triantafyllou ’05.  Mini-Lecture: SNR

Feb 13


Naselaris ‘06

Feb 15

Oxygen consumption:

Thompson ‘05

Feb 20

Local field potentials:

Mini-Lecture: image acquisition. Logothetis ‘01

Feb 22


Nedergaard ‘03

Feb 27

Energy budgets:

Attwell ’01, Lennie ‘03

Mar 1

Negative BOLD:

Devor ‘05, Shmuel ‘06

Mar 6

Demo experiment

Meet at CMRR

Mar 8

Final project definitions

5-minutes presentations for each student, describing scope of final project, 2 primary references

Mar 20


Mini-lecture:  linear systems analysis.
Boynton ‘96

Mar 22


Heckman ‘07

Mar 27

Sample data

Meet at CMRR

Mar 29


No paper assigned. Experiment Design.

Apr 3


Oakes ’05; Smith ‘99

Apr 5


(analysis outside of class)

Apr 10


Weiskopf ‘07

Apr 12


Q&A – data analysis on BLiSS.

Apr 17

General linear model:

Mini-lecture: GLM.  Buxton Ch. 18

Apr 19

Noise and error:

FDR - Genovese ‘02

Apr 24

Final Presentations

Each student will complete an in-depth literature review on a topic selected (and approved by the instructor) no later than the Mar. 8 meeting. Students will spend ~30 min. presenting their findings and submit an annotated bibliography (8 – 10 references).

Apr 26

May 1

May 3