MRI Physics 2: Contrasts and Protocols   Chris Rorden Types of contrast: Protocols – – – – Static: T1, T2, PD Endogenous: T2* BOLD (‘fMRI’), DW Exogenous: Gadolinium Perfusion Motion: ASL www.fmrib.ox.ac.uk/~karla/ www.hull.ac.uk/mri/lectures/gpl_page.html www.cis.rit.edu/htbooks/mri/chap-8/chap-8.htm www.e-mri.org/cours/Module_7_Sequences/gre6_en.html MR Contrast – a definition  We use different MRI protocols that are dominated by different contrasts  Contrasts influence the brightness of a voxel  For example, water (CSF) is relatively dark in a T1-weighted scan, but relatively bright in a T2 scan MR Contrast  Four types of MR contrasts: Static Contrast: Sensitive to relaxation properties of the spins (T1, T2) Endogenous Contrast: Contrast that depends on intrinsic property of tissue (e.g fMRI BOLD) Exogenous contrast: Contrast that requires a foreign substance (e.g Gadolinium) Motion contrast: Sensitive to movement of spins through space (e.g perfusion) Anatomy of an MRI scan    Place object in strong magnetic field: atoms align to field Transmit Radio frequency pulse: atoms absorb energy Wait Listen to Radio Frequency emission due to relaxation Wait, Goto Time between set and is our Echo Time (TE) Time between step being repeated is our Repetition Time (TR) TR and TE influence image contrast TE Time TR T1 and T2 definitions  T1-Relaxation: – – Recovery of longitudinal orientation ‘T1 time’ refers to interval where 63% of longitudinal magnetization is recovered  T2-Relaxation: – – Recovery Dephasing Loss of transverse magnetization ‘T2 time’ refers to interval where only 37% of original transverse magnetization is present Contrast: T1 and T2 Effects Fat: Short T1 1 CSF: Long T1 0 TR (s) CSF: Long T2 Signal  T1 effects measure recovery of longitudinal magnetization T2 refers to decay of transverse magnetization T1 and T2 vary for different tissues For example, fat has very different T1/T2 than CSF This difference causes these tissue to have different image contrast T1 is primarily influenced by TR, T2 by TE Magnetization    Fat: Short T2 TE (s) 0.2 T1 Effects: get them while their down  Consider very short TR: Fat has rapid recovery, each RF pulse will generate strong signal Water has slow recovery, little net magnetization to tip Before first pulse: 1H in all tissue strongly magnetized T1 effects explain why we discard the first few fMRI scans: the signal has not saturated, so these scans show more T1 than subsequent images After several rapid pulses: CSF has little net magnetization, so these tissue will not generate much signal Fat CSF Signal Decay Analogy  After – – – RF transmission, we can detect RF emission Emission at Larmor frequency Emissions amplitude decays over time Analogous to tuning fork: frequency constant, amplitude decays Relaxation  After RF absorption ends, protons begin to release energy – – – – Emission at Larmor frequency Emissions amplitude decays over time Different tissues show different rates of decay ‘Free Induction Decay’ (FID)  Strongest signal immediately after transmission  Therefore, we always want a short TE? TE and T2 contrast Signals from all tissue decays with time Signal decays faster in some tissues than others Optimal contrast between tissue when they emit relatively different signals Optimal GM/WM contrast White Matter: Fast Decay Signal Signal Gray Matter: Slow Decay TE (s) Contrast: difference between GM and WM signal TE (s) 10 Field Inhomogeneity Artifacts      When we put an object (like someone’s head) inside a magnet, the field becomes non-uniform When the field is inhomogeneous, we will get artifacts: resonance frequency will vary across image Prior to our first scans, the scanner is ‘shimmed’ to make the field as uniform as possible Shimming is difficult near air-tissue boundaries (e.g., sinuses) Shimming artifacts more intense at higher fields 17 Spin Echo Sequence echo sequences apply a 180º refocusing pulse half way between initial 90º pulse and measurement  This pulse eliminates phase differences due to artifacts, allowing measurement of pure T2  Spin echo dramatically increases signal Actual Signal T2 Signal  Spin T2* 0.5 TE 0.5 TE Time 18 Spin Echo Sequences  The refocusing pulse allows us to recover true T2  Image from – – www.e-mri.org/cours/Module_4_Signal/contraste1_en.html Web site includes interactive adjustment of T1/T2 T2 T2* 19 Analogy for Spin Echo Consider two clocks – –   Simultaneously,set both clocks to read 12:00 (~ 420º send in 90º RF pulse) Wait precisely one hour –   Clock 1: minute hand takes 70 minutes to make a revolution Clock 2: minute hand takes 55 minutes to make a revolution Minute hands now differ: out of phase Minute hand rotation  Reverse direction of each clock (~ send in 180º RF pulse) Wait precisely one hour – – Minute hands now identical: both read noon They are briefly back in phase hour hour 20 T2*: fMRI Signal is an artifact  fMRI is ‘Blood Oxygenation Level Dependent’ measure (BOLD)  Brain regions become oxygen rich after activity: ratio of Hbr/HbrO2 decreases 21 BOLD effect  Deoxyhemoglobin (Hbr) acts as contrast agent  Frequency spread causes signal loss over time  Effect increases with delay (TE = echo time) But, overall signal reduces with TE Optimal BOLD TE ~60ms for 1.5T, ~30ms at 3T www.fmrib.ox.ac.uk/~karla/ Fera et al (2004) J MRI 19, 19-26 Low Frequency TE (s) 0.2 High 22 BOLD artifacts  fMRI is a T2* image – we will have all the artifacts that a spin-echo sequence attempts to remove  Dephasing near air-tissue boundaries (e.g., sinuses) results in signal dropout Non-BOLD BOLD www.fmrib.ox.ac.uk/~karla/ 23 Optimal fMRI scans    More observations with shorter TR, but slightly less signal per observation (due to T1 effects and temporal autocorrelation) When you have a single anatomical region of interest use the fewest slices required for a very short TR For exploratory group study, use a scan that covers whole brain with minimal spatial distortion (for good normalization) – – Typical 3T: 3x3x3mm 64x64 matrix, 36 slices, SENSE r=2, TE=35ms, TR= 2100ms Typical 1.5T: 3x3x3mm 64x64 matrix, 36 slcies, TE=60ms, TR= 3500ms •Shorter TR yields better SNR •Diminishing returns •G.H Glover (1999) ‘On Signal to Noise Ratio Tradeoffs in fMRI’ 24 Diffusion Imaging  Diffusion imaging is an endogenous contrast  Apply two gradients sequentially with opposite polarity  Stationary tissue will be both dephased and rephased, while spins that have moved will be dephased  Sensitive to acute stroke (DWI, see lesion lecture)  Multiple directions can measure white matter integrity (diffusion tensor imaging, see DTI lecture) water diffuses faster in unconstrained ventricles than in white matter 25 Gadolinium Enhancement  Gd Perfusion scans are an example of an exogenous contrast – intravenously-injected  Gd – – – not detected by MRI (1H) Gd has an effect on surrounding 1H Gd shortens T1, T2, T2* of surrounding tissue makes vessels, highly vascular tissues, and areas of blood leakage appear brighter  Very rare side effect: allergic reaction  Gd can help measure perfusion – Useful for clinical studies: how much blood is getting to a region, how long does it take to get there? 26 Time of Flight     ToF is a motion contrast In T1 scans, motion of blood between slices can cause artifacts ToF intentionally magnifies flow artifacts Several Protocols of ToF, E.G: Flow Unsaturated Spins SLICE Use very short TR, so signal in slice is saturated External spins flowing into slice have full magnetization Conduct a Spin Echo Scan Except, 90º and 180º inversion pulses applied to different slices Only nuclei that travel between slices show coherent signal Saturated Spins 27 Arterial Spin Labelling z (=B0) excitation y www.fmrib.ox.ac.uk/~karla/ inversion slab blood x inversion  ASL   imaging plane white matter = low perfusion Gray matter = high perfusion is an example of a motion contrast IMAGEperfusion = IMAGEuninverted – IMAGEinverted Perfusion is useful for clinical studies: how much blood is getting to a region, how long does it take to get there? 28 Common Neuroimaging Protocols  T1 scans: high resolution, good gray-white matter contrast: VBM lecture  T2/DW scans: permanent brain injury: lesion lecture  Gd scans: acute brain dysfunction: lesion lecture  DTI scans: white matter fiber tracking: DTI lecture  T2*/ASL scans: scans for brain activity: most of this course 29 Advanced Physics Notes  We described 2D images using a 90º flip angle and spin echo for refocusing – – The very short TR of our T1 3D sequences use smaller flip angle with gradient echo refocusing Optimal flip angle = Ernst angle It is calculated from the TR value and the T1 of tissue 30 Advanced Physics Notes  Field strength influences T1 and T2  Optimal TR/TE for contrast will depend on field strength – – Higher Field = Faster T2 decay: Typically, TE decreases as field increases = faster imaging Higher Field = Slower T1 recovery: TR must increase with field strength Influences T1 contrast: e.g time of flight improves improves with field strength 3.0T Scanner Signal 1.5T Scanner Magnetization 0 TE (s) TR (s) 31