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Section 2 Basic fMRI Physics. Other Resources These slides were condensed from several excellent online sources. I have tried to give credit where appropriate.

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Presentation on theme: "Section 2 Basic fMRI Physics. Other Resources These slides were condensed from several excellent online sources. I have tried to give credit where appropriate."— Presentation transcript:

1 Section 2 Basic fMRI Physics

2 Other Resources These slides were condensed from several excellent online sources. I have tried to give credit where appropriate. If you would like a more thorough introductory review of MR physics, I suggest the following: Robert Cox’s slideshow, (f)MRI Physics with Hardly Any Math, and his book chapters online. See “Background Information on MRI” section Mark Cohen’s intro Basic MR Physics slides Douglas Noll’s Primer on MRI and Functional MRI For a more advanced tutorial, see: Joseph Hornak’s Web Tutorial, The Basics of MRI

3 Recipe for MRI 1) Put subject in big magnetic field (leave him there) 2) Transmit radio waves into subject [about 3 ms] 3) Turn off radio wave transmitter 4) Receive radio waves re-transmitted by subject – Manipulate re-transmission with magnetic fields during this readout interval [ ms: MRI is not a snapshot] 5) Store measured radio wave data vs. time – Now go back to 2) to get some more data 6) Process raw data to reconstruct images 7) Allow subject to leave scanner (this is optional) Source: Robert Cox’s web slidesRobert Cox’s web slides

4 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

5 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

6 Necessary Equipment MagnetGradient CoilRF Coil Source: Joe Gati, photos RF Coil 4T magnet gradient coil (inside)

7 x 80,000 = 4 Tesla = 4 x 10,000  0.5 = 80,000X Earth’s magnetic field Robarts Research Institute 4T The Big Magnet Very strong Continuously on Source: 1 Tesla (T) = 10,000 Gauss Earth’s magnetic field = 0.5 Gauss Main field = B 0 B0B0

8 Magnet Safety The whopping strength of the magnet makes safety essential. Things fly – Even big things! Screen subjects carefully Make sure you and all your students & staff are aware of hazzards Develop stratetgies for screening yourself every time you enter the magnet Do the metal macarena! Source: flying_objects.html

9 Subject Safety Anyone going near the magnet – subjects, staff and visitors – must be thoroughly screened: Subjects must have no metal in their bodies: pacemaker aneurysm clips metal implants (e.g., cochlear implants) interuterine devices (IUDs) some dental work (fillings okay) Subjects must remove metal from their bodies jewellery, watch, piercings coins, etc. wallet any metal that may distort the field (e.g., underwire bra) Subjects must be given ear plugs (acoustic noise can reach 120 dB) This subject was wearing a hair band with a ~2 mm copper clamp. Left: with hair band. Right: without. Source: Jorge Jovicich

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

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

12 Radio Frequency

13 Larmor Frequency Larmor equation f =  B 0  = MHz/T At 1.5T, f = MHz At 4T, f = MHz Field Strength (Tesla) Resonance Frequency for 1H

14 RF Excitation Excite Radio Frequency (RF) field transmission coil: apply magnetic field along B1 (perpendicular to B 0 ) for ~3 ms oscillating field at Larmor frequency frequencies in range of radio transmissions B 1 is small: ~1/10,000 T tips M to transverse plane – spirals down analogies: guitar string (Noll), swing (Cox) final angle between B 0 and B 1 is the flip angle B1B1 B0B0 Source: Robert Cox’s web slidesRobert Cox’s web slides Transverse magnetization

15 Cox’s Swing Analogy Source: Robert Cox’s web slidesRobert Cox’s web slides

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

17 T1 and TR Source: Mark Cohen’s web slidesMark Cohen’s web slides T1 = recovery of longitudinal (B 0 ) magnetization used in anatomical images ~ msec (longer with bigger B0) TR (repetition time) = time to wait after excitation before sampling T1

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

19 Precession In and Out of Phase Source: Mark Cohen’s web slidesMark Cohen’s web slides 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

20 T2 and TE Source: Mark Cohen’s web slidesMark Cohen’s web slides 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)

21 Echos Source: Mark Cohen’s web slidesMark Cohen’s web slides 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* pulse sequence: series of excitations, gradient triggers and readouts Gradient echo pulse sequence 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

22 T1 vs. T2 Source: Mark Cohen’s web slidesMark Cohen’s web slides

23 T2* Source: Jorge Jovicich time M xy M o sin  T2T2 T2*T2* T 2 * relaxation dephasing of transverse magnetization due to both: - microscopic molecular interactions (T 2 ) - spatial variations of the external main field  B (tissue/air, tissue/bone interfaces) exponential decay (T 2 *  ms, shorter for higher B o )

24 Susceptibility Source: Robert Cox’s web slidesRobert Cox’s web slides Adding a nonuniform object (like a person) to B 0 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 Susceptibility variations can also be seen around blood vessels where deoxyhemoglobin affects T2* in nearby tissue

25 Hemoglobin Source: Jorge Jovicichhttp://wsrv.clas.virginia.edu/~rjh9u/hemoglob.html Hemoglogin (Hgb): - four globin chains - each globin chain contains a heme group - at center of each heme group is an iron atom (Fe) - each heme group can attach an oxygen atom (O 2 ) - oxy-Hgb (four O 2 ) is diamagnetic  no  B effects - deoxy-Hgb is paramagnetic  if [deoxy-Hgb]   local  B 

26 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 time M xy Signal M o sin  T 2 * task T 2 * control TE optimum S task S control SS Source: Jorge Jovicich

27 BOLD signal Source: Doug Noll’s primer

28 First Functional Images Source: Kwong et al., 1992

29 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

30 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

31 K-Space Source: Traveler’s Guide to K-space (C.A. Mistretta)Traveler’s Guide to K-space

32 A Walk Through K-space 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 both halves of k-space in 1 sec 1 st half of k-space in 0.5 sec 2 nd half of k-space in 0.5 sec vs. single shottwo shot 1st volume in 1 sec interpolated image Note: The above is k-space, not slices 1 st half of k-space in 0.5 sec 2 nd half of k-space in 0.5 sec 2nd volume in 1 sec


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