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

2012 spring, fMRI: theory & practice 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

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

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

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

The First “Brain Imaging Experiment” … and probably the cheapest one too! E = mc2 ??? 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

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? less likely but more amusing explanation: subjects got nervous when fast-talking doctors suggested an NMR most likely explanation: nuclear has bad connotations 2012 spring, fMRI: theory & practice

2012 spring, fMRI: theory & practice 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 2012 spring, fMRI: theory & practice Ogawa

First fMRI paper Flickering Checkerboard Brain Activity Time  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

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

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

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

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

2012 spring, fMRI: theory & practice 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 B0 Robarts Research Institute 4T x 80,000 = Source: www.spacedaily.com 2012 spring, fMRI: theory & practice

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

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

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

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 T1-WEIGHTED ANATOMICAL IMAGE T2-WEIGHTED ANATOMICAL IMAGE

2012 spring, fMRI: theory & practice 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

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

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

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

Review Magnetic field Tissue protons align with magnetic field (equilibrium state) RF pulses Protons absorb RF energy (excited state) Relaxation processes Spatial encoding using magnetic field gradients 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

Susceptibility Artifacts T2*-weighted image T1-weighted image sinuses ear canals -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

2012 spring, fMRI: theory & practice 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

2012 spring, fMRI: theory & practice 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

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

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

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

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