Contrast Mechanisms in MRI Introduction to Cardiovascular Engineering Michael Jay Schillaci, PhD Managing Director, Physicist Tuesday, September 16 th, 2008

Overview  Image Acquisition Basic Pulse Sequences Unwrapping K-Space Image Optimization  Contrast Mechanisms Static and Motion Contrasts  T1 & T2 Weighting, Field Strength, T2*, Dephasing Endogenous Contrasts  BOLD Imaging Motion Contrasts  Time of Flight, Diffusion, Perfusion

Basic Pulse Sequences

Image Formation  Integrate magnetization to get MRI signal  Select a z “slice” and form image of XY plane variations  Contrast from difference in magnetization in different tissues — Image at several times to get average Horizontal density Vertical density 

Basic MRI Scan Terminology  Orientation: Coronal Sagittal Axial  Matrix Size: # of Voxels in dimension  Field of view (FOV): Spatial extent of dimension  Resolution: FOV/Matrix size. Axial Orientation 64x64 Matrix 192x192mm FOV 3x3mm Resolution Sagittal Orientation 256x256 Matrix 256x256mm FOV 1x1mm Resolution CoronalSagittalAxial

Image Creation  The scanning process 1. Protocol sets Gradients and Encodes K-Space Weights 2. Signal is Determined with Fourier Transform 3. Image Created with Inverse Transform Step 1 Step 2 Step 3

Image Acquisition G y varies in each cycle Data Acquisition (DAQ)

 Gradient Field Ensures Field Greater on “Top”  Larmor Frequency Depends on z Position  RF pulse Energizes “Matched” Slice Slice Selection Gradient: G sl Field Strength Z Position

Frequency Encoding Gradient: G ro  Apply transverse gradient when we wish to acquire image.  Slice emits signal at Larmor frequency, e.g. lines at higher fields will have higher frequency signals. X Position Field Strength

Phase Encoding Gradient: G pe  Apply Orthogonal RF pulse Apply before readout Adjusts the phase along the dimension (usually Y) Y Position Field Strength

Unwrapping K-Space Image Adapted from Prof. Yao Wang’s Medical Imaging course notes at: Pixel Size: Field of View: Choose phase encoding time so that

Image Optimization  Adjustment of Flip Angle Parameter  Maximum SNR typically between 30 and 60 degrees  Long TR sequences (2D)  Increase SNR by increasing flip angle  Short TR sequences (TOF & 3D)  Decrease SNR by increasing flip angle Maximizing the signal gives the: Ernst Angle:

1.Assume perfect “spoiling” - transverse magnetization is zero before each excitation: 2.Spin-Lattice (T1) Relaxation occurs between excitations: 1.Assume steady state is reached during repeat time (TR): 2.Spoiled gradient rephases the FID signal at echo time (TE): Gradient Echo Imaging

Spin Echo Imaging  Spin echo sequence applies a 180º “refocusing pulse” Half way between 90º pulse and DAQ Allows measurement of true T2 time T2 T2*

The “Refocusing Pulse” Signal 0 1 T2 T2* 0.5 TE Actual Signal Spins Rotate at Different RatesRefocusing Pulse Re-Aligns Spins

1mm Gap 2mm Thick Volume Reconstruction  3D volumes composed of 2D slices  Slice thickness. Thicker slices have more hydrogen so more signal (shorter scan time) Thinner slices provide higher resolution (longer scan time)  Optional: gap between slices. Reduces RF interference (SNR) Fewer slices cover brain 3mm

Static Contrast Mechanisms

T1 and T2 Weighting  T1 Contrast Echo at T2 min Repeat at T1 max  T2 Contrast Echo at T2 max Repeat at T1 min  Net Magnetization is T1 Contrast Weighting T2 Contrast Weighting TE TRTE TR Min T2 ContrastMax T1 Contrast Max T2 ContrastMin T1 Contrast

Static Contrast Images T2 Weighted Image (T2WI) (Gray Matter – CSF Contrast) T1 Weighted Image (T1WI) (Gray Matter – White Matter)  Examples from the Siemens 3T “Anatomical Image” “Diagnostic Image”

Flip Angle Variation  RF Pulse Magnitude Determines Flip Angle Duration and magnitude are important  Adapted from: B0B0 M BCBC MZMZ  +z +x +y M XY

Field Strength Effects  Increased field strength Net magnetization in material is greater Increased contrast means signal is increased Image 1 resolution is better 1 MRI adapted from: Muscle Tissue

Tissue Contrast and Dephasing  Dephasing of H 2 O and Fat MRI signal is a composite of Fat and H 2 O signals H 2 O and Fat resonate at different frequencies  T1 F = 210 ms, T1 W = 2000 ms ( T1 F > T1 W → fat is brighter) Relative phase gives TE dependence Anti-Parallel (Φ FW = 180 o TE = ms Parallel ( Φ FW = 0 o TE = ms Φ FW MFMF MWMW

Endogenous Contrast

BOLD Imaging  Blood Oxyenation Level Dependent Contrast dHb is paramagnetic, Hb is less Susceptibility of blood increases linearly with oxygenation BOLD subject to T2* criteria  Oxygen is extracted from capillaries Arteries are fully oxygenated Venous blood has increased proportion of dHb Difference between Hb and dHb is greater for veins Therefore BOLD is result of venous blood changes

Sources of the BOLD Signal Neuronal activity Metabolism Blood flow Blood volume [dHb] BOLD signal BOLD is a very indirect measure of activity…

Neuronal Origins of BOLD Adapted from Logothetis et al. (2002) BOLD response predicted by dendritic activity (LFPs) Increased neuronal activity results in increased MR (T2*) signal LFP=Local Field Potential; MUA=Multi-Unit Activity; SDF=Spike-Density Function

BASELINE ACTIVE The BOLD Signal

BASELINEACTIVE BOLD Imaging  Blood Oxyenation Level Dependent Contrast Susceptibility of blood changes with oxygenation Blood flow correlated with task performance Differential activations can be mapped

Static Contrast - T2* Relaxation  T2* accounts for magnetic defects and effects T2 is relaxation due to spin-spin interaction of nuclei T2 M is relaxation induced by inhomogeneities of main magnet T2 MS is relaxation induced by magnetic susceptibility of material

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. BOLD Non-BOLD

Motion Contrast

Flow Weighting Time-of-Flight Contrast No Flow Medium Flow High Flow No Signal Medium Signal High Signal Vessel Acquisition Saturation Excitation Vessel

 Diffusion Coefficients  Magnitude (ADC) Maps “Proton pools”  Direction (Anisotropy) Maps “Velocity”  Reconstruct Fiber Tracks with “Clustering” Diffusion Tensor Imaging ADC Anisotropy

FA Vector MD Indices of Diffusion Anisotropy Relative anisotropy: Fractional anisotropy:

Healthy DTI in Stroke Research  Examine integrity of fiber tracts Tractography - trace white matter paths in gray matter Assess neglect as a disconnection syndrome Stroke

Arterial Spin Labeling  Perfusion Flow of fluid into vessels to supply nutrients/oxygen The amount and direction of flow matters

AlternatingInversion Pulsed Labeling Alternating Inversion Imaging Plane FAIR Flow-sensitive Alternating IR EPISTAR EPI Signal Targeting with Alternating Radiofrequency

ASL Pulse Sequences RF Gx Gy Gz Image 90 o 180 o Alternating opposite Distal Inversion Odd Scan Even Scan 180 o RF Gx Gy Gz Image 90 o 180 o Alternating Proximal Inversion Odd Scan Even Scan FAIR EPISTAR Flow-sensitive Alternating IR EPI Signal Targeting with Alternating Radiofrequency