2012 spring fMRI: theory & practice Class 2: Basics of fMRI 2012 spring fMRI: theory & practice

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

2012 spring fMRI: theory & practice The Briefest Possible Explanation of MR Physics I Could Manage (while still covering important ideas and jargon) 2012 spring fMRI: theory & practice

Necessary Equipment Magnet Gradient Coil RF Coil (inside) Magnet Gradient Coil RF Coil Source for Photos: Joe Gati 2012 spring fMRI: theory & practice 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 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 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 T2-WEIGHTED ANATOMICAL IMAGE T1-WEIGHTED ANATOMICAL IMAGE 2012 spring fMRI: theory & practice

Protons Can measure nuclei with odd number of neutrons 1H, 13C, 19F, 23Na, 31P 1H (proton) abundant: high concentration in human body high sensitivity: yields large signals 2012 spring fMRI: theory & practice 2012 spring fMRI: theory & practice

Protons align with field Outside magnetic field Protons align with field randomly oriented Inside magnetic field spins tend to align parallel or anti-parallel to B0 net magnetization (M) along B0 spins precess with random phase no net magnetization in transverse plane only 0.0003% of protons/T align with field M longitudinal axis Longitudinal magnetization transverse plane 2012 spring fMRI: theory & practice 2012 spring fMRI: theory & practice Source: Mark Cohen’s web slides M = 0 Source: Robert Cox’s web slides

Precession In and Out of Phase protons precess at slightly different frequencies because of (1) random fluctuations in the local field at the molecular level that affect both T2 and T2*; (2) larger scale variations in the magnetic field (such as the presence of deoxyhemoglobin!) that affect T2* only. over time, the frequency differences lead to different phases between the molecules (think of a bunch of clocks running at different rates – at first they are synchronized, but over time, they get more and more out of sync until they are random) as the protons get out of phase, the transverse magnetization decays this decay occurs at different rates in different tissues 2012 spring fMRI: theory & practice Source: Mark Cohen’s web slides 2012 spring fMRI: theory & practice

Turn your dial to 4T fMRI -- Broadcasting at a frequency of 170.3 MHz! Radio Frequency Turn your dial to 4T fMRI -- Broadcasting at a frequency of 170.3 MHz! 2012 spring fMRI: theory & practice 2012 spring fMRI: theory & practice

Larmor Frequency Larmor equation f = B0  = 42.58 MHz/T At 1.5T, f = 63.76 MHz At 4T, f = 170.3 MHz 170.3 Resonance Frequency for 1H 63.8 1.5 4.0 Field Strength (Tesla) 2012 spring fMRI: theory & practice 2012 spring fMRI: theory & practice

RF Excitation Excite Radio Frequency (RF) field transmission coil: apply magnetic field along B1 (perpendicular to B0) for ~3 ms oscillating field at Larmor frequency frequencies in range of radio transmissions B1 is small: ~1/10,000 T tips M to transverse plane – spirals down analogies: guitar string (Noll), swing (Cox) final angle between B0 and B1 is the flip angle Transverse magnetization 2012 spring fMRI: theory & practice 2012 spring fMRI: theory & practice Source: Robert Cox’s web slides

Relaxation and Receiving Receive Radio Frequency Field receiving coil: measure net magnetization (M) readout interval (~10-100 ms) relaxation: after RF field turned on and off, magnetization returns to normal longitudinal magnetization  T1 signal recovers transverse magnetization  T2 signal decays 2012 spring fMRI: theory & practice 2012 spring fMRI: theory & practice Source: Robert Cox’s web slides

T1 and TR T1 = recovery of longitudinal (B0) magnetization used in anatomical images ~500-1000 msec (longer with bigger B0) TR (repetition time) = time to wait after excitation before sampling T1 2012 spring fMRI: theory & practice 2012 spring fMRI: theory & practice Source: Mark Cohen’s web slides

T2 and TE T2 = decay of transverse magnetization TE (time to echo) = time to wait to measure T2 or T2* (after refocussing with spin echo or gradient echo) 2012 spring fMRI: theory & practice 2012 spring fMRI: theory & practice Source: Mark Cohen’s web slides

T2* T2* relaxation dephasing of transverse magnetization due to both: - microscopic molecular interactions (T2) - spatial variations of the external main field B (tissue/air, tissue/bone interfaces) exponential decay (T2*  30 - 100 ms, shorter for higher Bo) Mxy Mo sin T2 T2* time 2012 spring fMRI: theory & practice 2012 spring fMRI: theory & practice Source: Jorge Jovicich

Echos pulse sequence: series of excitations, gradient triggers and readouts Gradient echo pulse sequence Echos – refocussing of signal Spin echo: use a 180 degree pulse to “mirror image” the spins in the transverse plane when “fast” regions get ahead in phase, make them go to the back and catch up measure T2 ideally TE = average T2 Gradient echo: flip the gradient from negative to positive make “fast” regions become “slow” and vice-versa measure T2* ideally TE ~ average T2* t = TE/2 A gradient reversal (shown) or 180 pulse (not shown) at this point will lead to a recovery of transverse magnetization TE = time to wait to measure refocussed spins 2012 spring fMRI: theory & practice Source: Mark Cohen’s web slides 2012 spring fMRI: theory & practice

T1 vs. T2 2012 spring fMRI: theory & practice Source: Mark Cohen’s web slides

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 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 2012 spring fMRI: theory & practice

Spatial Coding:Gradients Field Strength (T) ~ z position Freq Gradient coil add a gradient to the main magnetic field Spatial Coding:Gradients How can we encode spatial position? Example: axial slice excite only frequencies corresponding to slice plane Use other tricks to get other two dimensions left-right: frequency encode top-bottom: phase encode Gradient switching – that’s what makes all the beeping & buzzing noises during imaging! 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

A Walk Through K-space single shot EPI two shot EPI single shot spiral two shot spiral (forgive the hand drawn spirals) Note: The above is k-space, not slices echo-planar imaging sample k-space in a linear zig-zag trajectory spiral imaging sample k-space in a spiral trajectory single shot imaging sample k-space with one trajectory multi-shot imaging sample k-space with multiple (typically 2 or 4) trajectories Our technicians at RRI prefer spiral and multishot acquisitions because they’re more efficient 2012 spring fMRI: theory & practice 2012 spring fMRI: theory & practice

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

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

2012 spring fMRI: theory & practice A Walk Through K-space single shot two shot K-space can be sampled in many “shots” (or even in a spiral) 2 shot or 4 shot less time between samples of slices allows temporal interpolation Note: The above is k-space, not slices both halves of k-space in 1 sec 1st half of k-space in 0.5 sec 2nd half of k-space in 0.5 sec 1st half of k-space in 0.5 sec 2nd half of k-space 2nd volume in 1 sec vs. interpolated image 1st volume in 1 sec 2012 spring fMRI: theory & practice

Susceptibility Adding a nonuniform object (like a person) to B0 will make the total magnetic field nonuniform This is due to susceptibility: generation of extra magnetic fields in materials that are immersed in an external field For large scale (10+ cm) inhomogeneities, scanner-supplied nonuniform magnetic fields can be adjusted to “even out” the ripples in B — this is called shimming Susceptibility Artifact -occurs near junctions between air and tissue sinuses, ear canals -spins become dephased so quickly (quick T2*), no signal can be measured sinuses ear canals Aha! Susceptibility variations can also be seen around blood vessels where deoxyhemoglobin affects T2* in nearby tissue 2012 spring fMRI: theory & practice 2012 spring fMRI: theory & practice Source: Robert Cox’s web slides