Class 3: Introduction of fMRI

1. Class 3: Introduction of fMRI 2012 spring, fMRI: theory & practice

2. Outline • part 1 • Introduction of MRI and fMRI • Physics and BOLD • MRI safety, experimental design, etc • part 2 • BVQX installation, sample dataset, GSG manual, and forum, etc overview • Q&A 2012 spring, fMRI: theory & practice

3. MRI vs. fMRI Functional MRI (fMRI) studies brain function. MRI studies brain anatomy. 2012 spring, fMRI: theory & practice

4. Brain Imaging: Anatomy CAT PET Photography MRI 2012 spring, fMRI: theory & practice Source: modified from Posner & Raichle, Images of Mind

5. MRI vs. fMRI MRI fMRI high resolution (1 mm) low resolution (~3 mm but can be better) one image … • fMRI • Blood Oxygenation Level Dependent (BOLD) signal • indirect measure of neural activity many images (e.g., every 2 sec for 5 mins)  neural activity   blood oxygen   fMRI signal 2012 spring, fMRI: theory & practice

6. E = mc2 ??? The First “Brain Imaging Experiment” … and probably the cheapest one too! Angelo Mosso Italian physiologist (1846-1910) “[In Mosso’s experiments] the subject to be observed lay on a delicately balanced table which could tip downward either at the head or at the foot if the weight of either end were increased. The moment emotional or intellectual activity began in the subject, down went the balance at the head-end, in consequence of the redistribution of blood in his system.” -- William James, Principles of Psychology (1890) 2012 spring, fMRI: theory & practice

7. most likely explanation: nuclear has bad connotations less likely but more amusing explanation: subjects got nervous when fast-talking doctors suggested an NMR History of NMR • NMR = nuclear magnetic resonance • Felix Block and Edward Purcell • 1946: atomic nuclei absorb and re-emit radio frequency energy • 1952: Nobel prize in physics • nuclear: properties of nuclei of atoms • magnetic: magnetic field required • resonance: interaction between magnetic field and radio frequency Bloch Purcell NMR  MRI: Why the name change? 2012 spring, fMRI: theory & practice

8. History of fMRI MRI -1971: MRI Tumor detection (Damadian) -1973: Lauterbur suggests NMR could be used to form images -1977: clinical MRI scanner patented -1977: Mansfield proposes echo-planar imaging (EPI) to acquire images faster fMRI -1990: Ogawa observes BOLD effect with T2* blood vessels became more visible as blood oxygen decreased -1991: Belliveau observes first functional images using a contrast agent -1992: Ogawa et al. and Kwong et al. publish first functional images using BOLD signal Ogawa 2012 spring, fMRI: theory & practice

9. First fMRI paper Flickering Checkerboard OFF (60 s) - ON (60 s) -OFF (60 s) - ON (60 s) - OFF (60 s) Brain Activity 2012 spring, fMRI: theory & practice Time  Source: Kwong et al., 1992

10. The Continuing Rise of fMRI # of Publications Year of Publication Done on Jan 13, 2012 2012 spring, fMRI: theory & practice

11. fMRI Setup 2012 spring, fMRI: theory & practice

12. fMRI intro movie 2012 spring, fMRI: theory & practice

13. Necessary Equipment 4T magnet RF Coil gradient coil (inside) Magnet Gradient Coil RF Coil Source for Photos: Joe Gati 2012 spring, fMRI: theory & practice

14. B0 The Big Magnet • Very strong • 1 Tesla (T) = 10,000 Gauss • Earth’s magnetic field = 0.5 Gauss • 4 Tesla = 4 x 10,000  0.5 = 80,000X Earth’s magnetic field • Continuously on • Main field = B0 Robarts Research Institute 4T x 80,000 = Source: www.spacedaily.com 2012 spring, fMRI: theory & practice

15. Metal is a Problem! Source: www.howstuffworks.com Source: http://www.simplyphysics.com/ flying_objects.html “Large ferromagnetic objects that were reported as having been drawn into the MR equipment include a defibrillator, a wheelchair, a respirator, ankle weights, an IV pole, a tool box, sand bags containing metal filings, a vacuum cleaner, and mop buckets.” -Chaljub et al., (2001) AJR 2012 spring, fMRI: theory & practice

16. Step 1: Put Subject in Big Magnet Protons (hydrogen atoms) have “spins” (like tops). They have an orientation and a frequency. When you put a material (like your subject) in an MRI scanner, some of the protons become oriented with the magnetic field. 2012 spring, fMRI: theory & practice

17. Step 2: Apply Radio Waves When you apply radio waves (RF pulse) at the appropriate frequency, you can change the orientation of the spins as the protons absorb energy. After you turn off the radio waves, as the protons return to their original orientations, they emit energy in the form of radio waves. 2012 spring, fMRI: theory & practice

18. Step 3: Measure Radio Waves T1 measures how quickly the protons realign with the main magnetic field T2 measures how quickly the protons give off energy as they recover to equilibrium fat has high signal  bright fat has low signal  dark CSF has high signal  bright CSF has low signal  dark 2012 spring, fMRI: theory & practice T2-WEIGHTED ANATOMICAL IMAGE T1-WEIGHTED ANATOMICAL IMAGE

19. Jargon Watch • T1 = the most common type of anatomical image • T2 = another type of anatomical image • TR = repetition time = one timing parameter • TE = time to echo = another timing parameter • flip angle = how much you tilt the protons (90 degrees in example above) 2012 spring, fMRI: theory & practice

20. Step 4: Use Gradients to Encode Space field strength space lower magnetic field; lower frequencies higher magnetic field; higher frequencies Remember that radio waves have to be the right frequency to excite protons. The frequency is proportional to the strength of the magnetic field. If we create gradients of magnetic fields, different frequencies will affect protons in different parts of space. 2012 spring, fMRI: theory & practice

21. Step 5: Convert Frequencies to Brain Space k-space contains information about frequencies in image We want to see brains, not frequencies 2012 spring, fMRI: theory & practice

22. K-Space 2012 spring, fMRI: theory & practice Source: Traveler’s Guide to K-space (C.A. Mistretta)

23. Review Magnetic field Tissue protons align with magnetic field (equilibrium state) RF pulses Protons absorb RF energy (excited state) Spatial encoding using magnetic field gradients Relaxation processes Relaxation processes Protons emit RF energy (return to equilibrium state) NMR signal detection Repeat RAW DATA MATRIX Fourier transform 2012 spring, fMRI: theory & practice IMAGE Source: Jorge Jovicich

24. sinuses ear canals Susceptibility Artifacts T2*-weighted image T1-weighted image • -In addition to T1 and T2 images, there is a third kind, called T2* = “tee-two-star” • -In T2* images, artifacts occur near junctions between air and tissue • sinuses, ear canals • In some ways this sucks, but in one way, it’s fabulous… 2012 spring, fMRI: theory & practice

25. What Does fMRI Measure? • Big magnetic field • protons (hydrogen molecules) in body become aligned to field • RF (radio frequency) coil • radio frequency pulse • knocks protons over • as protons realign with field, they emit energy that coil receives (like an antenna) • Gradient coils • make it possible to encode spatial information • MR signal differs depending on • concentration of hydrogen in an area (anatomical MRI) • amount of oxy- vs. deoxyhemoglobin in an area (functional MRI) 2012 spring, fMRI: theory & practice

26. BOLD signal Blood Oxygen Level Dependent signal • neural activity   blood flow   oxyhemoglobin   T2*  MR signal Source: fMRIB Brief Introduction to fMRI 2012 spring, fMRI: theory & practice

27. Hemodynamic Response Function • % signal change • = (point – baseline)/baseline • usually 0.5-3% • initial dip • -more focal and potentially a better measure • -somewhat elusive so far, not everyone can find it • time to rise • signal begins to rise soon after stimulus begins • time to peak • signal peaks 4-6 sec after stimulus begins • post stimulus undershoot • signal suppressed after stimulation ends 2012 spring, fMRI: theory & practice

28. BOLD signal 2012 spring, fMRI: theory & practice Source: Doug Noll’s primer

29. The Concise Summary We sort of understand this (e.g., psychophysics, neurophysiology) We sort of understand this (MR Physics) We’re *&^%$#@ clueless here! 2012 spring, fMRI: theory & practice

30. Spatial and Temporal Resolution Gazzaniga, Ivry & Mangun, Cognitive Neuroscience 2012 spring, fMRI: theory & practice