1. fMRI Methods Lecture1 - Introduction

2. http://www. weizmann. ac. il/neurobiology/labs/malach/ilan ilan
Leonesco Bldg. room 208

3. Course overview
Go over syllabus Weekly exercises, final project (grades) Office hours Groups Scanning (safety, Helsinki) Matlab (experience, licenses) Huettel et. al.

4. Imaging
Contrast
Resolution
(spatial, temporal)

5. Resolution scales

6. MRI scanner
What is the measurement in this image?

7. Hydrogen atoms

8. Static magnetic field direction
Physics
Static magnetic field direction

9. Physics

10. The voxel

11. First anatomical MRI 106 voxels took 4 hours to scan!
Damadian et. al. 1977

12. Anatomy 1T 2T

13. Anatomical measures
Gray/White matter
Cortical thickness

14. Diffusion tensor imaging (DTI)

15. Blue: up-down Green: fwd-bwd Yellow: right-left
Tractography
Blue: up-down Green: fwd-bwd Yellow: right-left

16. Tractography

17. So far we didn’t care about temporal resolution.

18. Neurovascular coupling
Heeger et. al. 2002

19. Hemodynamics

20. Hemodynamic changes
Time
Heeger et. al. 2002

21. Hemodynamic response

22. Experiment

23. Experiment

24. scan/volume fMRI R L
Front
Back
24 slices every 1.5 seconds

25. fMRI activation maps Motor system
When judging about stimulus speed there are differences in motor/decision areas

26. fMRI activation maps
Visual
system
Motor system

27. Obsession with localization!
fMRI activation maps
Visual
system
Motor system
Obsession with localization!

28. With fMRI we care about temporal resolution. Temporal sampling rate
With fMRI we care about temporal resolution. Temporal sampling rate. Limited by Hemodynamics

29. Break

30. Matlab
A tool for manipulating vectors and matrices. Matlab offers an immense number of functions with which one can do these manipulations quickly. Generally we will assume that our data (neural and hemodynamic responses) are generated by a linear system. What does it mean to be linear?

31. Linearity
A linear system is one that satisfies the following two conditions: 1. Additivity/Superposition – f(x+y) = f(x) + f(y) 2. Homogeneity – f(ax) = af(x) What does this mean?

32. a*x + b*y + c*z scaling/weighting
Example of a linear system
a*x + b*y + c*z scaling/weighting Y
Stimulus and
neural response:
X (stimulus) = a*Y (neural response) X

33. Example of a non-linear system
The response of a single neuron at any given time is non-linear. It’s an all or nothing response with a certain threshold – a spike. A linear system has to output “graded” responses of consistently increasing/decreasing amplitudes. However, the summed response of a neuron across time windows of a given length (i.e. compute its firing rate) may be linear….

34. Example of a non-linear system
The response of a single neuron at any given time is non-linear. It’s an all or nothing response with a certain threshold – a spike. A linear system has to output “graded” responses of consistently increasing/decreasing amplitudes. However, the summed response of a neuron across time windows of a given length (i.e. compute its firing rate) may be linear….

35. Are incredibly useful ways of representing data...
Vectors and matrices
Are incredibly useful ways of representing data...
For example images of the brain

36. Are incredibly useful ways of representing data...
Vectors and matrices
Are incredibly useful ways of representing data...
Or sound – voltage changes over time

37. And for manipulating the data...
Vectors and matrices
And for manipulating the data...
How would you increase the volume of this sound segment?

38. Go over handout Open Matlab getting started section
“Geometric” linear algebra
Go over handout Open Matlab getting started section

39. Matlab Tutorials
Open a folder for your code on the local computer. Try to keep the path name simple (e.g. “C:\Your_name”). Download code and MRI data from: Save Lab1.zip in the folder you’ve created and unzip. Open Matlab. Change the “current directory” to the directory you’ve created. Open: “Lab1_VisualizingBrain.m” When done open: “Lab1_CreatingStimuli.m”

40. Homework!
Read Chapters 1 & 2 of Huettel et. al. (available in library) Review Geometric linear algebra handout Matlab exercise: me the report as a word document. The report should include answers, figures, and the actual Matlab code used to generate them (copy it into word). This week, don’t forget to also send me the movie you’ve created.