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

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

3 credits

 

Please see the tentative syllabus for the course description and topics that will be covered.

 

Syllabus

 

Interesting Links

 

Different people have different ways of explaining MRI.  Here are some that have been helpful.

     Jeff Hornak’s MRI Web-book

     Brian Hargreaves’ animations of spin physics

     MR-TIP, a resource for MR professionals

Please suggest the addition of any links/resources you like.

 

Ideas for Midterm Project

Weekly assignments

 

 

Date

Topic

Due Date

WA1

Jan 17

Neurons per voxel calculation

Jan 24

WA2

Jan 24

Balloon model:  CBF, CBV, CMRO2

Jan 31

WA3

Jan 31

Image contrast

Feb 7

WA4

Feb 7

k-space:  kspace1.mat (.txt) (.dat)
                kspace2.mat (.txt) (.dat)

Feb 14

 

Feb 14

Drop-out and fieldmaps

 

WA5

Feb 21

Distortion and total read-out time: fm.mat (.txt) (.dat)

Feb 28

WA6

Feb 28

Programming assignment:  local and voxel-average BOLD model for given neural “activity”

Mar 9

WA7

Mar 21

Experiment design model

Mar 28

WA8

Mar 28

SNR and CNR

Apr 4

WA9

Apr 4

Data formats and file I/O

  epi.img   epi.hdr DICOM file  (all 3 zipped)

Apr 11

 

 

Programming assignment:  ROI selection

 

WA10

Apr 18

Programming assignment: GLM analysis tool

Apr 25

 

 

Programming assignment:  confidence intervals

 

 

 

In-class Exercises/Examples

 

 

Lecture

Topic

ICE1

Jan 19

Energy budgets

ICE2

Jan 26

Balloon model

ICE3

Feb 2

Steady-state longitudinal magnetization

 

 

Matlab FFT tutorial code.  zebras.mat

ICE4

Feb 9

Fourier transform examples

ICE5

Feb 16

Distortion.  filesForWarping.mat

ICE6

Feb 23

SNR

ICE7

Mar 2

Programming example:  modeling neural “activity” and BOLD

ICE8

Mar 21

Final project example

ICE9

Mar 30

Data simulation.

  caoComputeTTA.m

  caoSimulateData.m

  caoMakeBlock.m

  caoMakeER.m

  caoMakeERms.m

  gbMseq.m

ICE10

Apr 6

Rotation matrices

ICE11

Apr 13

Programming example:  GLM, single voxels

ICE12

Apr 18

Programming example:  GLM, single voxels

ICE13

ICE13b

Apr 20

Programming example: deconvolution and trial-triggered averages

  caoMakeStimConvMtx.m

ICE15

Apr 27

Programming example:  confidence intervals

 

 

Past Lectures

 

Date

Topic

Jan 17

Introduction

Jan 19

Neurons, architecture, and energy budgets

Jan 24

Cell  metabolism, vascular architecture, and blood flow regulation

Jan 26

BOLD:  background, balloon model, and current topics

Jan 31

Magnetization, equilibrium, and relaxation

Feb 2

Hardware and pulse sequences

Feb 7

Gradients and k-space (no movies).  FLASH sequence movie.  EPI sequence movie.  Lecture with movies (.zip, 14MB).

Feb 9

Pulse sequence diagrams; slice selection and k-space

Feb 14

Pulse sequence diagrams and spin echo

Feb 16

Dropout

Feb 21

Distortion

Feb 23

SNR

Feb 28

Back to BOLD Basics

Mar 2

Localization I

Mar 9

Localization II and CBF

Mar 21

Final project assignment

Mar 28

SNR and CNR

Mar 30

Human subjects – SAR, dB/dt

Apr 4

Data formats; pre-processing

Apr 6

Motion compensation

April 11

Anatomical ROIs; alignment between functional and anatomical data

April 13

GLM: single voxel

April 18

GLM: multiple voxels

April 20

GLM: full model (comparison with TTA and assumed HIRF)

April 25

Significance and Confidence I

April 27

Significance and Confidence II