Lecture01_CourseIntro_MRIPhysics

Lecture01_CourseIntro_MRIPhysics - Analysis Methods in...

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Unformatted text preview: Analysis Methods in Functional Magnetic Resonance Imaging ECE 595-08 595• Hardware • Spin • Sequences Outline • MR Basic Principles • Review Syllabus (check Feb • Lecture 3rd class) • Basics of BOLD fMRI • Signal mechanism • Sequences used • Artifacts • A few trade-offs trade- Sprint 2009 fMRI Analysis Course 1 Sprint 2009 fMRI Analysis Course 2 Puzzle Pieces The Magnet • Goal: align the protons • Coils • Super conductance: Helium Helmholtz Golay • 1.5T, 3T, 7T 3T (Earth magnetic field = 0.0005T) • Side Effects (FDA : <8T, neonates <4T ) • • • • • 3 Sprint 2009 fMRI Analysis Course Nausea Vertigo Tingling Headache Pain in tooth fillings 4 Sprint 2009 fMRI Analysis Course Not harmful? • Goal: The Gradient Coils • Slice selection • Frequency encoding • Phase encoding Side Effects • • • • Sprint 2009 fMRI Analysis Course Induced currents (dynamo; small) Nerve stimulation Phosphenes Acoustic Noise 6 5 Sprint 2009 fMRI Analysis Course 1 The RF Coil • Goal: • Turn longitudinal magnetization into transverse magnetization • Measure the signal generated by the precessing spins. Head coil Coils Surface coil •highest signal at hotspot •high SNR at hotspot • Side Effects • Induced currents: Specific Absorption Rate (SAR) limits • Heating: avoid loops. •homogenous signal •moderate SNR Sprint 2009 fMRI Analysis Course 7 Sprint 2009 fMRI Analysis Course 8 Basic Theory • Protons have a property called spin • Larmor Equation: ω = γB0 • ω = Larmor frequency • γ = gyromagnetic ratio • 42MHz/T for protons (1H) 13 • 11MHz/T for 13C • 176GHz/T for electrons (e-) Basic Theory Sprint 2009 fMRI Analysis Course 9 Sprint 2009 fMRI Analysis Course 10 Basic Theory Basic Theory Sprint 2009 fMRI Analysis Course 11 Sprint 2009 fMRI Analysis Course 12 2 Basic Theory z Basic Theory 90° 180° Sprint 2009 fMRI Analysis Course 13 Sprint 2009 fMRI Analysis Course 14 Longitudinal Relaxation Time T1 Transverse Relaxation Time T2 Mz Mo Mxy 63% 1-e-t/T1 37% t T1 T2 t Longitudinal Relaxation = Energy transfer between excited spins and Tissue (Spin-Lattice-Relaxation) Reestablishing of longitudinal magnetization with time constant T1 Transverse Relaxation = Decay of magnetization by interaction between nuclei (Spin-Spin-Relaxation) Sprint 2009 fMRI Analysis Course 15 Sprint 2009 fMRI Analysis Course 16 T1-relaxation time T11.0 Relaxation Times are Tissue Specific Tissue 1 0.8 white matter T1 = 600 gray matter T1 = 1000 Tissue 1 Signal Mz S 0.6 0.4 0.2 0.0 0 CSF T1 = 3000 Tissue 2 Tissue 2 Short TE Medium TE Long TE TR Longitudinal Relaxation 1000 2000 3000 TR (msec) Transverse Relaxation • Depends on tissue type • • • White matter: 70 ms Gray matter: 90 ms CSF: 400 ms • Measure the signal 200 ms after the RF pulse. • • • White matter: e-200/70 = 5% 5% Gray matter: e-200/90 = 10% 10% CSF: e-200/400 = 60 60 Sprint 2009 fMRI Analysis Course 17 Sprint 2009 fMRI Analysis Course • T2 << T1 18 3 Image contrast z’ NMR Signal z’ z’ Long Proton Density B0 M0 y’ y’ y’ TR Short T2 X’ X’ X’ S(t) S(t) S0≈M0 S(t) T2* S(t) T1 poor! Short Sprint 2009 fMRI Analysis Course Long 0 t TE 19 T0=1/f0 Spin refocusing 90°x B0 z’ z’ 5 5 1 Spin echo 90° 180° t = TE/2 z’ 180°y z’ 4 1 2 z’ 32 2 4 2 y’ X’ X’ 3 y’ 3 X’ y’ X’ 5 4 1 y’ X’ y’ t=0 t = TE/2 t = TE Hahn echo CPMG (Carr-Purcell-Meiboom-Gill) modification : multiple t = TE Spin echo Gradient 90° T2* Gradient echo Gradient readout T2* 180° readout T2 Signal FID + Transversal 0 Moments Phase 5 4 1 2 3 3 2 1 4 5 Signal Spin echo Transversal Moments Phase FID gradient echo t t 4 Longitudinal Relaxation …. t=t0 B0 90° t=t1 Mz=0 t=t2 Mz=a t=t3 Mz=b t= Mz=1 Making an image 1. Slice selection with a gradient field B0+2 B0+1 B0 0 z Resonance at ω = γ(B0+ 1) M0 Mz(t) t0 t1 t2 t3 t a) Set a z-gradient b) Choose the frequency of the RF pulse c) Switch off the z-gradient Making an image 2. Frequency encoding with a gradient field Making an image 3. Phase encoding with a gradient field Bx 0 By 0 Phase advance Slower precession: slow changing signal Faster precession: fast changing signal x y b) Measure only fast signals c) Measure only slow signals a) When measuring the signal, set a gradient -> back of head -> front of head a) After the RF pulse, set a gradient for a brief time b) Measure the signal The phase of the signal depends on the y-position : sin(…+y) c) Repeat, with ever stronger gradient The signal : sin(…+2y), sin(…+3y), sin(…+4y) d) Signals that change rapidly with the repeat number have large y e) Signals that change slowly with the repeat number have small y Raw Data Matrix (k-Space) ky 1 2 N Fourier Transformation K_y y Raw data matrix or k-space is filled line by line by variation of the Phase Encoding Gradient kx Line Information = Frequencies of the Readout Gradient K_x Sprint 2009 fMRI Analysis Course x 29 Sprint 2009 fMRI Analysis Course 30 5 EPI imaging and k-space kx = frequency and y = phase or angle Frequency and phase encoding merely plots a trajectory across k-space. k- frequ. encode phase encode Sprint 2009 fMRI Analysis Course 31 Sprint 2009 fMRI Analysis Course 32 EPI and Spirals ky ky kx EPI kx Gx Gy Sprint 2009 fMRI Analysis Course Gx Gy 34 33 Sprint 2009 fMRI Analysis Course Outline EPI Susceptibility: Eddy currents: k = 0 is sampled: Corners of kspace: Gradient demands: Sprint 2009 fMRI Analysis Course Spirals blurring, dephasing blurring 1st no pretty high 35 • MR Basic Principles • Hardware • Spin • Sequences distortion, dephasing ghosts 1/2 through yes very high • Basics of BOLD fMRI • Signal mechanism • Sequences used • Artifacts • A few trade-offs trade- Sprint 2009 fMRI Analysis Course 36 6 Basics of BOLD fMRI The MR room Sprint 2009 fMRI Analysis Course 37 Sprint 2009 fMRI Analysis Course 38 Scanner Internals Macroscopic: Brain Systems Sprint 2009 fMRI Analysis Course 39 Sprint 2009 fMRI Analysis Course 40 Microscopic: Neuronal Function Hemodynamic Measure of Brain Function (1881) Arm Brain Action Potentials & Neurotransmitter Trafficking Sprint 2009 fMRI Analysis Course Angelo Mosso 41 Sprint 2009 fMRI Analysis Course Pressure Traces “Bertino” Bertino” 42 7 Blood Oxygen Level Dependent (BOLD) Neurons arterioles capillary bed Neuronal Firing venules arterioles capillary bed venules Artery Vein Baseline • • • • • 43 HbO2 Deoxy-Hb Deoxy- “Activated” Activated” Mxy Signal Arterioles Capillary Bed Venules 1 - 3 cm Sprint 2009 fMRI Analysis Course Neural activity increases Blood flow increases (“reactive hyperemia”) hyperemia” Deoxyhemoglobin concentration decreases Magnetic field homogeneity increases Gradient echo EPI signal increases Mo sin T2* task T2* control S time Stask Scontrol TEoptimum Sprint 2009 fMRI Analysis Course 44 Hemodynamic Response Properties • Magnitude of signal changes is quite small • • • 0.5 to 3% at 1.5 T (or smaller) Too small to see in individual images Always considering differences or time-course changes timein image intensity Blood Oxygen Level Dependent (BOLD) Contrast Activation • Response is delayed and quite slow (~10 seconds) • Extracting temporal information is tricky, but possible • Even short events have a rather long response Sprint 2009 fMRI Analysis Course 45 Sprint 2009 fMRI Analysis Course 46 Time-Course Response in fMRI Time• Brief neuronal events can elicit a (positive) blood flow and oxygenation response. • Reponses to events as brief as 50 ms have been recorded. Slower Start of Rise and Event Fall in ~10 s Negative Response Response to periodic flashes of light Processed Image Anatomic Image Functional MRI response to a visual stimulus of duration 2s Sprint 2009 fMRI Analysis Course 47 Sprint 2009 fMRI Analysis Course 48 8 Typical Functional Image Volume • • fMRI Experiment Stages: Prep 1) Prepare subject Consent form • Safety screening Instructions 2) Shimming putting body in magnetic field makes it non-uniform • • adjust 3 orthogonal weak magnets to make magnetic field as homogenous as possible 3) Sagittals Take images along the midline to use to plan slices Sprint 2009 fMRI Analysis Course 49 Sprint 2009 fMRI Analysis Course 50 Slice Terminology • • • Slice Thickness e.g., 6 mm fMRI Experiment Stages: Functionals 5) Take functional (T2*) images images are indirectly related to neural activity • usually low resolution images (3x3x5 mm) all slices at one time = a volume (sometimes also called an image) sample many volumes (time points) (e.g., 1 volume every 2 seconds for 150 volumes = 300 sec = 5 minutes) 4D data: 3 spatial, 1 temporal VOXEL (Volumetric Pixel) In-plane resolution e.g., 192 mm / 64 = 3 mm • 3 mm 3 mm SAGITTAL SLICE Number of Slices e.g., 10 6 mm IN-PLANE SLICE … first volume (2 sec to acquire) Matrix Size e.g., 64 x 64 Field of View (FOV) e.g., 19.2 cm Sprint 2009 fMRI Analysis Course 51 Sprint 2009 fMRI Analysis Course 52 MRI vs. fMRI high resolution (1 mm) fMRI process chain fMRI low resolution (~3 mm but can be better) MRI Functional Images Phase Fix Registration Time (secs) one image 1 2 3 … 750 2 13 .33s 0s .66s 1 2 fMRI Blood Oxygenation Level Dependent (BOLD) signal indirect measure of neural activity … many images (e.g., every 2 sec for 5 mins) Threshold/ Overlay Detection/ Estimation Normalization y Xβ e 1 53 Sprint 2009 fMRI Analysis Course neural activity Sprint 2009 fMRI Analysis Course blood oxygen fMRI signal 2 54 9 Functional images ~2s Activation Statistics fMRI Signal (% change) Stimulation protocols in fMRI baseline rest % signal change ROI Time Course time course of activation Time Co nd itio Condition n 1 Statistical Map superimposed on anatomical MRI image images Time Co nd itio stimulation n 2 ... haemodynamic response function Region of interest (ROI) Sprint 2009 fMRI Analysis Course ~ 5 min 55 Sprint 2009 fMRI Analysis Course 56 Statistical Maps & Time Courses Use stat maps to pick regions Then extract the time course 2D 3D Sprint 2009 fMRI Analysis Course 57 Sprint 2009 fMRI Analysis Course Sprint 58 Design Jargon: Runs session: all of the scans collected from one subject in one day run (or scan): one continuous period of fMRI scanning (~5-7 min) experiment: a set of conditions you want to compare to each other condition: one set of stimuli or one task Design Jargon: Paradigm or Protocol 4 stimulus conditions + 1 baseline condition (fixation) paradigm (or protocol): the set of conditions and their order used in a particular run run epoch: one instance of a condition first “objects right” epoch second “objects right” epoch A session consists of one or more experiments. Each experiment consists of several (e.g., 1-8) runs More runs/expt are needed when SNR is low or the effect is weak. Thus each session consists of numerous (e.g., 5-20) runs (e.g., 0.5 – 3 hours) Sprint 2009 fMRI Analysis Course volume #1 (time = 0) epoch 8 vol x 2 sec/vol = 16 sec volume #105 (time = 105 vol x 2 sec/vol = 210 sec = 3:30) Time 59 Sprint 2009 fMRI Analysis Course 60 10 Susceptibility in MR All susceptibility effects increase with Bo field Susceptibility in Temporal Lobes The good. The bad. The ugly. Sprint 2009 fMRI Analysis Course 61 Sprint 2009 fMRI Analysis Course 62 What is the source of susceptibility? Bo Susceptibility effects occur near magnetically dis-similar materials dis- The magnet has a spatially uniform field but your head is magnetic… Pattern of B field outside magnetic object in a uniform field… Bo 1.5T 3T 1) deoxyHeme is paramagnetic 2) Water is diamagnetic ( = -10-5) 3) Air is paramagnetic ( = 4x10-6) Ping-pong ball in H20: Field maps (TE = 5ms), black lines spaced by 0.024G (0.8ppm at 3T) Sprint 2009 fMRI Analysis Course 63 Sprint 2009 fMRI Analysis Course 64 Bo map in head: it’s the air tissue interface… Other Sources of Susceptibility You Should Be Aware of… of… Sagittal Bo field maps at 3T Sprint 2009 fMRI Analysis Course Those fillings might be a problem… 65 Sprint 2009 fMRI Analysis Course 66 11 Local susceptibility gradients: 2 effects Sagittal Bo field map at 3T Bandwidth is asymmetric in EPI (Distortion is 100x more in phase direction) ky • Local dephasing of the signal (signal loss) within a voxel, mainly from thru-plane gradients Local geometric distortions, (voxel location improperly reconstructed) mainly from local in-plane gradients (in PE direction). • The phase error (and thus distortions) are in the phase encode direction. = kx t=0.5ms t=0.005ms Sprint 2009 fMRI Analysis Course 67 Sprint 2009 fMRI Analysis Course 68 Susceptibility in EPI can give either a compression or expansion Susceptibility Causes Image Distortion Use shortest possible encoding Altering the direction kspace is traversed causes either local compression or expansion. choose your poison… encode time 1/BW z Echoplanar Image, 3T head gradients 3T whole body gradients Sprint 2009 fMRI Analysis Course Field near sinus 69 Sprint 2009 fMRI Analysis Course Encode time = 34, 26, 22, 17ms 70 With fast gradients, add parallel imaging k 2 FOV 3T MAGNETOM Allegra ss EPI PAT ss Single shot TE = 30 ms Conventional 64x64 with PAT x2 64x64 { Reduced k-space sampling Acquisition: SMASH SENSE Folded images in each receiver channel Reconstruction: Folded datasets + Coil sensitivity maps Sprint 2009 fMRI Analysis Course with PAT x2 128x128 with PAT x2 192x128 4 channel tx/rx array coil 71 MAGNETOM Allegra. Courtesy Bruker Medical and USA Instruments. Sprint 2009 fMRI Analysis Course 72 12 What can you do? • • • • Good shimming (first & second order) Thinner slices (Drawback: Takes more to cover the brain) Shorter TE (Drawback: BOLD contrast is optimized for TE = T2*local) T2*local) “Z-shimming” Repeat measurement several times with an applied z shimming” gradients that rewind the dephasing, Pick the right gradient afterward on a dephasing, pixel by pixel basis. (Drawback: multi shot or longer encode). Yang et al. Yang MRM 39 p402, 1998. Use special RF pulse with built-in prephasing in just the right places. built(Drawback: long RF pulse, pre-phasing differs from person to person) preGlover et al. Proceed. ISMRM p298, 1998. Glover The “mouth shim” paramagnetic material in roof of mouth. Wilson, shim” Wilson, Jenkinson, Jezzard, Proceed. ISMRM p205, 2002. Jenkinson, Jezzard, Distortion correction based on a measured field map (drawback: cannot cannot recover signal dropout or fully correct “overlapping” intensities) overlapping” Multi-shot imaging methods (drawback: more motion sensitive) MultiFancy pulse sequences (best to have local physicist): 180 degree refocusing pulses to reverse distortion (GRASE)/Multiple refocusing refocusing pulses… single-shot FSE, U-Flare pulses… singleU73 Single-shot Gradient Echo EPI Single• Parameters you can choose • • • • • • • • TR Slice thickness/gap Number of slices/slice acquisition order TE Bandwidth Matrix size Field of view Flip angle • • • • • • All of these parameters can be appropriately applied over a wide range of values 74 Sprint 2009 fMRI Analysis Course Sprint 2009 fMRI Analysis Course TR (repetition time) • Determines how much magnetization is allowed to recover before it is knocked over again by the next rf pulse • From a pure signal strength perspective, waiting for very long TR’s (5 seconds +) allows for maximal TR’ signal-to-noise (SNR) signal- to• Noise is MR dominated by physiologic noise (not thermal noise) • Requires many images in both conditions to reliably distinguish activation (which requires shorter TR’s) TR’ • fMRI can be performed as fast as TR=100ms • Bottom line: use as short a TR as you can Sprint 2009 fMRI Analysis Course Flip Angle • A given flip angle will maximize the SNR (Ernst Angle)…at long TR’s (> 3s) this is 90 degrees Angle)… TR’ • This angle is dependent upon the TR • Incorrect angles may sensitize your BOLD scans to ininflow artifacts (bad) [Lu et al, NeuroImage 17, 943–955 (2002)] [Lu 943– • Bottom line: For TR of 1-2s, a flip angle of around 6016070 degrees is optimal cos 1 exp TR / T1 75 Sprint 2009 fMRI Analysis Course 76 Number of slices • Separate slices in EPI are typically squeezed into a TR interval • Many factors influence # of slices that fit in a TR • • • • Length of TR TE (determines center of blue box) Matrix size (determines length of blue box) Bandwidth (determines length of blue box) So far • • • • Long TR maximized SNR Short TR maximizes fMRI stats Long TR provides many slices Short TR provides few slices • Bottom line: collect as many slices as you can • The above suggests imaging only brain regions of interest (to minimize slices) • But processing decisions also play a role • Whole brain data is much easier to spatially normalize • Motion correction works best with thin slices • In general TR’s between 1s and 2s are not too bad TR’ Sprint 2009 fMRI Analysis Course 77 Sprint 2009 fMRI Analysis Course 78 13 Slice Thickness • SNR in MRI is proportional to voxel volume (thinner slices -> less SNR) • Thinner slices reduces partial volume effects • Thinner slices reduces through-plan dephasing through• What is the size of the structure of interest? • Isotropic voxel size is preferred TE (echo time) • Optimum TE is shorter at high field (say 30ms at 3T versus 50ms at 1.5T) • Shorter TE reduces signal loss due to field inhomogeneities, but also reduces BOLD effect Sprint 2009 fMRI Analysis Course 79 Sprint 2009 fMRI Analysis Course 80 Bandwidth • Rate at which points are sampled (the echoes are digitized) • High bandwidth implies a high sampling rate • Sampling of the order of 128 kHz • 128kHz/64matrix = 2000Hz/pixel Matrix Size • Matrix size impact everything • Increasing matrix size decreases voxel size and thus SNR • Increasing matrix and FOV maintains constant voxel size, but increases N and therefore increases SNR • Intravoxel dephasing reduced somewhat with smaller voxels (bigger matrix) • Noise is proportional to sampling rate • High bandwidth means faster data acquisition (and more slices can be acquired, with less T2 blurring) Sprint 2009 fMRI Analysis Course Sprint 81 Sprint 2009 fMRI Analysis Course 82 Field of View (FOV) • Voxel size determined by field of view and matrix size x FOVx Nx y FOVy Ny • FOV=200mm/64 matrix = 3.125mm voxel dimension • Recall SNR proportional to voxel volume Sprint 2009 fMRI Analysis Course 83 14 ...
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