Class 1: Introduction of fMRI 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

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

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

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

E = mc 2 ??? The First “Brain Imaging Experiment” “[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) Angelo Mosso Italian physiologist ( ) … and probably the cheapest one too! 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 BlochPurcell NMR  MRI: Why the name change? most likely explanation: nuclear has bad connotations less likely but more amusing explanation: subjects got nervous when fast-talking doctors suggested an NMR 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 Ogawa 2012 spring, fMRI: theory & practice

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

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

fMRI Setup 2012 spring, fMRI: theory & practice

fMRI intro movie 2012 spring, fMRI: theory & practice

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

x 80,000 = Robarts Research Institute 4T The Big Magnet Source: 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 B0B spring, fMRI: theory & practice

Metal is a Problem! Source: Source: 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 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 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 CSF has low signal  dark T1-WEIGHTED ANATOMICAL IMAGE T2-WEIGHTED ANATOMICAL IMAGE fat has low signal  dark CSF has high signal  bright 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 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. lower magnetic field; lower frequencies higher magnetic field; higher frequencies space field strength 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

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

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

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

BOLD signal Source: fMRIB Brief Introduction to fMRIfMRIB Brief Introduction to fMRI  neural activity   blood flow   oxyhemoglobin   T2*   MR signal Blood Oxygen Level Dependent signal 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

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

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

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