http://www.magnet.fsu.edu Disclosure Advanced Neuro MRI: Imaging Techniques and Protocol Optimization Research funding provided by Siemens Healthcare. Chen Lin, PhD DABR Indiana University School of Medicine & Indiana University Health MRI, 35 year ago MRI Today Patent 3789832 filed 17 March 1972, issued Feb 5, 1974 First MR scan (image) of the human body on July 3, 1977 2D Multi slice -> 3D Isotropic Static -> Dynamic, Real-time Anatomical -> Functional Qualitative -> Quantitative Advanced Functional MRI Exam High res 3D anatomical scan 3D T1 MP-RAGE (IR-SPGR) 3D T2 or FLAIR SPACE (CUBE) DSC or ASL Perfusion BOLD fmri Motor (finger tapping, object handling) Speech (Rhyming, Naming, Word Generation) Memory DTI Spectroscopy CEST, T1-rho, MTC MRA / MRV Outlines Echo Planar Image (EPI) EPI pulse sequence. Variants of EPI. Characteristics of EPI. Common artifacts associated with EPI. EPI based Techniques BOLD-fMRI, DTI, DSC, ASL. Challenges and requirements. Optimizing imaging parameters. 1
Single-shot GRE (GRE/FID-EPI) K-space Sampling in EPI Gslice ~90 0 ~90 0 TR ~ Exp(-TE/T 2 *) Gread E1 E2 E3 E4 E5 E6 GRE Train (~64) Gphase Blip Gphase Constant Phase Encoding: sum of all previous G phase pulse areas Blip E8 E7 E6 E5 E4 E3 E2 E1 Constant Covering the ENTIRE K-space after one RF excitation E8 E7 E6 E5 E4 E3 E2 E1 Variants of EPI Spin Echo EPI (SE-EPI) ~90 0 180 0 ~90 0 TE/2 TE/2 GRE-EPI SE-EPI Gslice Gread GRASE Gphase T 2 weighted contrast with SE-EPI instead of T 2 * weighted for GRE-EPI Reduced off-resonance artifacts Blip Gslice Gread Gphase GRASE ~90 0 180 0 180 0 180 0 ~90 0 Characteristics of EPI Fast and efficient scan. freeze motion Low SAR compared with SS-FSE. Artifact prone More severe @ higher field strength Requires high performance and well calibrated hardware. Limited spatial resolution T2*w for GRE-EPI; T2w for SE-EPI and GRASE. 2
Common Problems in EPI Second Look T2 TSE SE EPI Geometric Distortion in EPI Chemical Shift Artifact in EPI Gread Without Fat Suppression With Fat Suppression Gphase B 0 inhomogeneity introduces local gradients Gread Phase error accumulates in the echo train. Minimized with fewer echoes (ETL) and/or less echo spacing (ESP) Retrospective correction with measured B 0 map Low sampling rate in phase direction Low bandwidth -> Large chemical shift in phase direction Inversely proportional to Echo SPacing (ESP) Nyquist (N/2) Ghosting How to reduce Echo SPacing (ESP) FOV/2 EPI Increase receiver BW (Faster sampling rate) Reduce read-out resolution (Less frequency encoding points) Different phase shifts in odd and even frequency encoding lines Correct by: Gradient calibration and/or eddy current compensation Reference scan (w/o phase encoding or shifting one phase step) Use ramp sampling 3
How to reduce Echo Train Length (ETL) EPI Protocol Optimization Reduce phase resolution or phase FOV (Less phase encoding steps) Partial Phase Fourier Parallel Imaging Partial Fourier How to reduce Geometric Distortion and Chemical Shift in EPI? 1. Reduce FOV 2. Reduce receiver BW 3. Reduce TE 4. Reduce acquisition matrix size EPI Protocol Optimization How to reduce Geometric Distortion (GD) and Chemical Shift (CS) artifact in EPI? 1. FOV -> rbw -> ESP -> GD & CS. 2. rbw -> ESP -> GD & CS. Examples with varying ESP & ETL rbw=752hz/px p=none rbw=1502hz/px p=none 3. TE -> Susceptibility Artifact, but GD & CS should remain the same. 4. Matrix size -> ETL -> GD & CS, but Spatial Resolution. rbw=752hz/px p=2 rbw=1502hz/px p=2 Multi-shot EPI (MS-EPI) SS-EPI versus MS-EPI 1 8 16 32 Single-shot EPI (SS-EPI) with low resolution in phase direction Interleaved multi-shot EPI (MS- EPI) with higher resolution 8 4 2 1 Multi-shot -> Less echoes per shot -> reduced susceptibility artifacts (distortion). 4
Source: Functional Magnetic Resonance Imaging Signal [%] 3/30/2013 Holdsworth SJ Eur J Radiol. 2008 Jan;65(1):36-46 Readout Segmented EPI (RS-EPI) SS-EPI versus RS-EPI Advanced Neuro MRI Techniques Based on EPI Acquisition Neuro-activity and Blood Oxygenation 1. BOLD functional MRI (fmri) 2. Diffusion Weighted Imaging (DWI) Diffusion Tensor Imaging (DTI) 3. Perfusion Weighted Imaging (PWI) Dynamic Susceptibility Contrast (DSC ) Arterial Spin Labeling (ASL) Rest Active More deoxygenated Hb Deoxy-hemoglobin is paramagnetic (An endogenous contrast agent, like Gd) Increase of blood flow and oxygenated Hb Blood Oxygen Level Dependence (BOLD) Effect Resting State Oxyhemoglobin Signal Activated State Deoxyhemoglobin Signal change ~ 1-2 % @ 1.5T Activated Rest 30ms Chen Lin, TE PhD DABR 3/13 Increase in cerebral blood supply to the region of activation. Less increase of local oxygen extraction. Net reduction in deoxyhemoglobin concentration. Longer T2*. Increase of signal intensity in T2* weighted images such as GRE-EPI. on off Stimulus (Block Design) EPI Volume Series BOLD fmri Modeled Response Measured Signal Changes 4.5 3 1.5 0-1.5 0 20 40 60 80 100 120 140 160 180 Time [s] Statistical Significance of Correlation 5
Typical fmri Setup fmri Post processing Sync Trigger Console Area Scanner Room Response Recording Stimulus Presentation Timing correction Motion correction Statistical analysis Co-registration Function map overlay Fiber-optic cables Equipment Room Typical BOLD fmri Protocol @ 3T GRE-EPI, TE = 30ms, TR (min) = ~2000ms FOV = 224mm, Matrix = 64x64 (3.5mm x 3.5mm) 33 slices of 3.5mm and 0 gap (whole brain coverage) Use high receiver bandwidth (e.g. > 2000 Hz/Px) Fat Suppression Parallel Imaging 144 volumes (16 volumes/block) in 4:52 Reduce patient motion and use Prospective Motion Correction (Siemens 3D PACE) BOLD fmri for Surgical Planning Restricted Water Diffusion in Tissue Diffusion Weighted SE-EPI 90 0 180 0 RF G s G R G P G d S/S b=0 = e badc where b = g 2 G 2 d 2 ( - d/3) 6
Diffusion Anisotropy and DTI l 1 Fractional Anisotropy (FA) Color Scheme l 1 l3 l2 l 3 FA Map Intensity = FA Value Color = Fiber Direction l 2 Isotropic Beaulieu (2002). NMR in Biomed; 15:435-455 Anisotropic Color FA Map SLF cc CR Red: right - left Green: anterior - posterior Blue: superior - inferior DWI of different diffusion sensitizing directions DTI based Fiber Tracking / Tractography Provide information about white matter connectivity Typical Brain DTI Protocol SE-EPI, TE = min, with TR > 4000 ms,. FOV = 224mm; Matrix: 128x128 (2.0mmx2.0mm) 64 slices of 2.0mm and 0 gap (whole brain coverage) Use high receiver bandwidth (e.g. > 1500 Hz/Px) Fat Suppression Parallel Imaging (2) and partial Fourier (6/8). b = 0 and >1000 sec/mm 2, 12-30 directions for FA, > 64 directions for Tracking (~10 min) Reduce patient motion and use Prospective Motion Correction (Siemens 3D PACE) Comparison of DTI Fiber Tracking with Histology Preparation Fiber Tracking and Neurosurgical Planning. S. Mori - JHU 7
Perfusion Perfusion Model and Parameters v Artery Capillary Bed Vein Deliver oxygen and nutrients to the cells Affected by pathological and physiological conditions, such as tumor angio-genesis, stroke and infarct, vascular wall changes. Blood Flow (ml of blood / gram of tissue / sec) Blood Volume (ml of blood / gram of tissue) Mean Transit Time (MTT) (sec) CBF = CBV / MTT MR Perfusion Imaging Methods Dynamic Susceptibility Contrast (DSC) MRI Perfusion GRE-EPI (T2* weighted) SE-EPI (T2 weighted) Dynamic Contrast Enhanced (DCE) MRI Perfusion Spoiled Fast Gradient Echo (T1 Weighted) Arterial Spin Labeling Dynamic Susceptibility Contrast (DSC) Perfusion Imaging Signal Baseline Time To Peak Time To Minimum Mean Transit Time Negative Enhancement Integral Percent Baseline at Peak Time DSC Perfusion Maps DSC Perfusion Maps Relative Mean Transit Time (relmtt) Percent Baseline at Peak (PBP) Relative Mean Transit Time (relmtt) Relative Cerebral Blood Flow (RELCBF) Time to Peak (TTP) Negative Enhancement Integral (NEI) Time to Peak (TTP) Relative Cerebral Blood Volume (RELCBV) 8
Typical DSC Perfusion Protocol Single-shot GRE-EPI or SE-EPI TE = 30 60 ms (GRE-EPI) or 50 80 ms (SE-EPI) TR = min. ( < 2 sec depends on number of slices ) 10-12 slices of 5.0 mm and 0 gap (lesion coverage) Use high receiver bandwidth (e.g. > 1500 Hz/Px) Fat Suppression and partial Fourier (6/8). TA = 90-120 sec. or ~ 100 time points (10-30 time points pre-contrast) Contrast dose = 0.1 0.2 mmol/kg Injection rate: 3 5 ml/sec with 20 ml saline flush. SE-EPI vs GRE-EPI for DSC PWI SE-EPI signal (T2 dependent) is more specific to microvasculature/perfusion while GRE-EPI signal (T2* dependent) is also affected by larger vessels. GRE-EPI provides greater sensitivity and coverage/temporal resolution (more slices for same TR). DSC PWI Applications See what s behind the clouds Brain Tumor Case Surgical Planning of Brain Tumor 3D T2 FLAIR DSC Rel MTT DSC Rel CBV DSC TTP 9
Metal Artifact in EPI Summary Fast imaging techniques based on EPI acquisition enable advanced MRI applications including BOLD fmri, DTI, DSC and ASL Perfusion. EPI is artifact prone. Careful consideration and optimization of imaging parameters are needed to achieve accurate results. Thank You! www.indiana.edu/~mri 10