1. Institute for Biomedical Engineering EXCITE Afternoon Hands-On MRI Sessions: fMRI & DTI

2. Institute for Biomedical Engineering Contrast in MRI - Relevant Parameters Relaxation times:  T1Spin-lattice relaxation time (longitudinal relaxation time) Return of spin system to equilibrium state  T2Spin-spin relaxation time (transverse relaxation time) Loss of phase coherence due to fluctuations of interacting spins (‘phase memory time’)  T2*Decay time of free induction decay Signal loss due to magnetic field inhomogeneity (difference in magnetic susceptibility)  ADCApparent diffusion coefficient Signal loss due to diffusion of water molecules in an inhomogeneous magnetic field  kwater exchange rate Exchange of water between macromolecule bound fraction and bulk (free) water

3. Institute for Biomedical Engineering Sensitivity: Signal-to-Noise Ratio (SNR) Spatial resolution Temporal resolution Signal: magnetization (number of spins, magnetic field strength, …. ) Noise: thermal noise of receiver system, physiological noise, … Relations and Limitations

4. Institute for Biomedical Engineering IBT MRI Contrast

5. Institute for Biomedical Engineering  MRI delivers good soft tissue contrast  Tissue specific magnetic parameters for contrast generation  T2 / T2*: how fast is signal lost after excitation  T1: how fast is magnetization gained back after excitation for next experiments  Sequence parameters and sequence type determine contrast Relaxation times

6. Institute for Biomedical Engineering 0 0.5 1.0 +1.0 0.0 time (s) M i (t)/M eq MxMx MyMy MzMz The NMR signal Relaxation exp(-t/T 2 *) 1-exp(-t/T 1 )

7. Institute for Biomedical Engineering  Relevant parameters:  Repetition time (TR) = time between two excitations  Flip angle -> how much magnetization is left for next excitation  Strong T1 weighting for large flip angle and short TR T1 weighting M xy MzMz M zA M zB θ T 1 Relaxation during TR

8. Institute for Biomedical Engineering T1 weighting: Example  Two metabolites with T1=500ms (blue) and T1=250ms (red)  Flip angle: 60°  Signal proportional to  M z  TR=3000ms 01.04.20108IBT time MzMz

9. Institute for Biomedical Engineering T1 weighting: Example  Two metabolites with T1=500ms (blue) and T1=250ms (red)  Flip angle: 60°  Signal proportional to  M z  TR=300ms 01.04.20109IBT time MzMz

10. Institute for Biomedical Engineering T1 weighting: Example  Two metabolites with T1=500ms (blue) and T1=250ms (red)  Flip angle: 60°  Signal proportional to  M z  TR=100ms 01.04.201010IBT time MzMz

11. Institute for Biomedical Engineering  Relevant parameter:  Echo time (TE) = time between excitations and data acquisition  Strong T2 weighting for long TE T2 / T2* weighting M xy t / ms TE short TE medium TE long

12. Institute for Biomedical Engineering  Intensity scales with number of signal generating nuclei per volume element  Keep influence of relaxation times small:  Short TE -> small effect of T2 / T2* on signal  Long TR -> small effect of T1 Proton density weighting

13. Institute for Biomedical Engineering IBT Functional MRI (fMRI)

14. Institute for Biomedical Engineering 14IBT  Uses echo planar imaging (EPI) for fast acquisition of T2*-weighted images.  Spatial resolution:  3 mm(standard 1.5 T scanner)  < 200 μm(high-field systems)  Sampling speed:  1 slice: 50-100 ms  Problems:  distortion and signal dropouts in certain regions  sensitive to head motion of subjects during scanning  Requires spatial pre-processing and statistical analysis. EPI (T2 * ) T1 dropout But what is it that makes T2* weighted images “functional”? Functional MRI (fMRI)

15. Institute for Biomedical Engineering The BOLD contrast Source: Jorge Jovicich, fMRIB Brief Introduction to fMRIfMRIB Brief Introduction to fMRI  neural activity   blood flow   oxyhemoglobin   T2*   MR signal REST ACTIVITY

16. Institute for Biomedical Engineering The temporal properties of the BOLD signal  sometimes shows initial undershoot  peaks after 4-6 secs  back to baseline after approx. 30 secs  can vary between regions and subjects Brief Stimulus Undershoot Initial Undershoot Peak

17. Institute for Biomedical Engineering IBT MRI and Diffusion

18. Institute for Biomedical Engineering Brownian motion  Molecules or atoms in fluids and gases move freely  Collisions with other particles causes trembling movement  Brownian motion: microscopic random walk of particles in fluids of gases (R. Brown 1827)  Brownian motion depends on thermal energy, particle properties and fluid density

19. Institute for Biomedical Engineering Diffusion  Diffusion: irreversible automatic mixing of fluids (or gases) due to Brownian motion  Root mean square displacement depends on diffusion coefficient D and time  (A. Einstein)  Diffusion coefficient D affected by cell membranes, organelles, macromolecules (Le Bihan 1995)

20. Institute for Biomedical Engineering Anisotropy  Restrictions on water diffusion usually without spherical symmetry  anisotropic diffusion in biological tissue  Diffusion tensor (=3x3-matrix) instead of diffusion coefficient accounts for anisotropic diffusion in 3D  Principal diffusion direction: direction with largest diffusion coefficient Free Diffusion Restricted Diffusion rr rr rr

21. Institute for Biomedical Engineering  Example: nerve fibre  Diffusion perpendicular to fibre restricted  Water diffusion indicates white matter organization

22. Institute for Biomedical Engineering Diffusion and MRI  Diffusion leads to signal loss in MRI

23. Institute for Biomedical Engineering Diffusion gradients  Signal attenuation depends on diffusion coefficient and gradient waveforms  GE: sum of diffusion weighting gradients zero  SE: diffusion weighting gradients have equal area  Single shot techniques freeze out physical motion TETE 90° 180° diffusion gradient diffusion gradient EPI readout

24. Institute for Biomedical Engineering Diffusion weighted imaging DWI  b-value (=b-factor) describes diffusion weighting analogous to TE in T2 weighted sequences  b-value determined by diffusion weighting gradients (i.e. gradient form, strength, distance) signal b-factor [s/mm 2 ] 0 2004006008001000 S0: signal without diffusion weighting; D: diffusion coefficient in direction of gradient

25. Institute for Biomedical Engineering DTI  Ellipsoid represents diffusion tensor  Fibre structure via map of diffusion anisotropy: calculate fractional anisotropy (or relative anisotropy or volume ratio) P M MP S MS PS DWIs + Reference    3D ellipsoid ADC FA Color- coded FA

26. Institute for Biomedical Engineering  Principal diffusion coefficient and vector: longest axis of diffusion tensor

27. Institute for Biomedical Engineering  Brain structures via analysis of principle diffusion vectors Optic radiation Pons Middle cerebellar peduncle Corticospinal tract Corpus callosum Medulla Superior cerebellar peduncle Superior longitudinal fasciculus Medulla Tapetum

28. Institute for Biomedical Engineering IBT MR Angiography

29. Institute for Biomedical Engineering 01.04.201029IBT Blood flow Image Slice Saturation: apply 90° slice-selective pulse Gradient echo imaging: Don’t wait for gradient echo  Bright signal from unsaturated spins in slice time Mz Stationary spins Inflowing spins saturation imaging MR Angiography