fMRI Methods Lecture1 - Introduction

1. fMRI MethodsLecture1 - Introduction

2. http://www.weizmann.ac.il/neurobiology/labs/malach/ilanilan.dinstein@weizmann.ac.ilLeonesco Bldg. room 208

3. Course overview Go over syllabusWeekly exercises, final project (grades)Office hoursGroupsScanning (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. 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. 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. Front R L Back scan/volumefMRI 24 slices every 1.5 seconds

25. fMRI activation maps Motor system

26. fMRI activation maps Visual system Motor system

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

28. 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. Example of a linear system a*x + b*y + c*zscaling/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. Vectors and matrices Are incredibly useful ways of representing data... For example images of the brain

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

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

38. “Geometric” linear algebra Go over handoutOpen 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:http://www.weizmann.ac.il/neurobiology/labs/malach/ilan/lecture_notes.htmlSave 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 handoutMatlab exercise: email 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.