fMRI Methods Lecture1 - Introduction
http://www. weizmann. ac. il/neurobiology/labs/malach/ilan ilan http://www.weizmann.ac.il/neurobiology/labs/malach/ilan ilan.dinstein@weizmann.ac.il Leonesco Bldg. room 208
Course overview Go over syllabus Weekly exercises, final project (grades) Office hours Groups Scanning (safety, Helsinki) Matlab (experience, licenses) Huettel et. al.
Imaging Contrast Resolution (spatial, temporal)
Resolution scales
MRI scanner What is the measurement in this image?
Hydrogen atoms
Static magnetic field direction Physics Static magnetic field direction
Physics
The voxel
First anatomical MRI 106 voxels took 4 hours to scan! Damadian et. al. 1977
Anatomy 1T 2T
Anatomical measures Gray/White matter Cortical thickness
Diffusion tensor imaging (DTI)
Blue: up-down Green: fwd-bwd Yellow: right-left Tractography Blue: up-down Green: fwd-bwd Yellow: right-left
Tractography
So far we didn’t care about temporal resolution.
Neurovascular coupling Heeger et. al. 2002
Hemodynamics
Hemodynamic changes Time Heeger et. al. 2002
Hemodynamic response
Experiment
Experiment
scan/volume fMRI R L Front Back 24 slices every 1.5 seconds
fMRI activation maps Motor system When judging about stimulus speed there are differences in motor/decision areas
fMRI activation maps Visual system Motor system
Obsession with localization! fMRI activation maps Visual system Motor system Obsession with localization!
With fMRI we care about temporal resolution. Temporal sampling rate With fMRI we care about temporal resolution. Temporal sampling rate. Limited by Hemodynamics
Break
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?
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?
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
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….
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….
Are incredibly useful ways of representing data... Vectors and matrices Are incredibly useful ways of representing data... For example images of the brain
Are incredibly useful ways of representing data... Vectors and matrices Are incredibly useful ways of representing data... Or sound – voltage changes over time
And for manipulating the data... Vectors and matrices And for manipulating the data... How would you increase the volume of this sound segment?
Go over handout Open Matlab getting started section “Geometric” linear algebra Go over handout Open Matlab getting started section
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.html 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”
Homework! Read Chapters 1 & 2 of Huettel et. al. (available in library) Review Geometric linear algebra handout Matlab 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.