1. Beyond the Standard EPI – New MRI Sequences available at the CBU Marta Morgado Correia MRC Cognition and Brain Sciences Unit Date

2. New Head Coil

3. 32 independent channels acquiring data simultaneously Image SNR is proportional to the square root of number of channels Upgrading from a 12 channel coil to a 32 channel coil results in increased SNR 32-Channel Coil Expected SNR gain: (would have to acquire ~2.7 times more data to see the same SNR increase with the 12 channel coil)

4. 12 vs 32 Channels - MPRAGE

5. 12 Channels32 Channels

6. 12 vs 32 Channels - MPRAGE 12 Channels32 Channels

7. 12 vs 32 Channels - MPRAGE 12 Channels32 Channels

8. 12 vs 32 Channels – T2 12 Channels32 Channels

9. 12 vs 32 Channels – Standard EPI 12 Channels32 Channels

10. 12 vs 32 Channels – DTI (b=0) 12 Channels32 Channels

11. 12 vs 32 Channels – DTI (b=1000) 12 Channels32 Channels

12. 12 vs 32 Channels – DTI (colour coded FA) 12 Channels32 Channels

13. 12 vs 32 Channels – SNR Comparison Expected SNR increase: sqrt(32/12)~1.63 Observed SNR increase: 1.18 -1.72

14. Other things you should know Auditory stimulus presentation available now Vision correction currently being developed (thanks to Gary) Haven’t yet found a volunteer that didn’t fit in the coil Using different padding is sometimes needed No time added to sequence acquisition time

15. Silent EPI S Schmitter (University of Heidelberg)

16. Silent EPI – S Schmitter (University of Heidelberg) MRI scanners generate high levels of acoustic noise during the process of image acquisition. The scanner noise is caused by mechanical vibrations of the gradient coils and other mechanical structures. Fast and heavy gradient switching, as in EPI, results in high noise levels. The EPI sequence developed by Schmitter et al. uses pure sinusoidal readout gradients and smoothed ramps for the remaining gradients.

17. Silent EPI imaging parameters Acquisition time: 2640ms (per volume) 32 slices in-plane resolution: 3x3mm 2 Slice thickness: 3mm + 25% gap (3.75mm) TE: 44ms 21 db quieter than standard EPI

18. Silent EPI Second level contrast (N=22), sound vs. silence. Annika Linke

19. Silent EPI There is slightly more drop out than in the standard EPI (due to the higher TE used). The TR is longer for 32 slices (TR=2640ms). The signal in auditory regions is the same or higher than obtained with the standard sequence. It is 21db quieter than the standard sequence which makes it worth it for auditory studies. Annika Linke

20. Multi-echo EPI B. Poser (Donders)

21. Multi-echo EPI – B Poser (Donders) Multiple images acquired at different values of TE. Signal loss due to field inhomogeneities increases with TE. The images acquired at the lower echo times show less signal loss in areas affected by susceptibility artefacts.

22. Multi-echo EPI – B Poser (Donders) TE=9.4 msTE=21.2 msTE=33 ms TE=57 msTE=45 ms

23. Multi-echo EPI – B Poser (Donders) Combined multi-echo EPI image (Simple average of different echoes. Other methods based on weighted averages accordingly to BOLD sensitivity also available – Setfan Hetzer and Rhodri Cusack).

24. Multi-echo EPI imaging parameters Acquisition time: 2470ms (per volume) 32 slices in-plane resolution: 3x3mm 2 Slice thickness: 3mm + 25% gap (3.75mm) TE: 9.4ms, 21.2ms, 33ms, 45 ms, 57ms ISSS version also available

25. 3D EPI B. Poser (Donders)

26. 3D vs 2D EPI Acquisition time: T 2D =N phase NEX T acq T 3D =N phase N slice NEX T acq T acq is the time that the data acquisition window is open during each readout (number of frequency encoded points divided by the full receiver bandwidth). SNR:

27. 3D vs 2D EPI Minimum slice thickness: For a 2D sequence the slice thickness is determined by the RF bandwidth,  f, and the gradient amplitude G : There are hardware limitations on G and  f, and therefore very thin slices cannot be achieved with a 2D sequence (>1.8mm for the Siemens product sequence). 3D should be used when very think slices are desired.

28. 3D EPI – B Poser (Donders) 3x3x3mm 3 TR=2100ms 32 slices 2x2x2mm 3 TR=2600ms 32 slices 1.5x1.5x1.5mm 3 TR=3100ms 32 slices

29. EPI sequence comparison Passive viewing of objects/scrambled objects vs. Fixation Rhodri Cusack

30. EPI sequence comparison The activation thresholded at p<0.001 uncorrected. The ME tends to give similar or a bit less power than the std EPI. The ME has less dropout (especially noticeable in the ofc). The 3D EPI also has less power even when smoothed and has a highly restricted field of view. Rhodri Cusack

31. High Resolution T2

32. T2-weighted structural Acquisition time: 4m 30 s 192 slices resolution: 1x1x1mm 3 Resolution and FOV matched to MPRAGE.

33. T1 vs (T1+T2) segmentation Histogram of GM probabilities for a single subject Jason Taylor

34. T1 vs (T1+T2) segmentation N = 7 Agreement across 2 sessions Adding T2 seems to help seg distinguish between GM and CSF T1 vs. T1+T2 Jason Taylor

35. Generalised Q-sampling Imaging

36. Generalised Q-sampling Imaging (GQI) The traditional diffusion tensor model assumes a single fibre orientation per voxel. Q-ball Imaging (QBI) and Diffusion Spectrum Imaging (DSI) remove this assumption and aim to reconstructed the full orientation distribution function (ODF) for each voxel. Traditionally these methods use a large number of directions (up to 500) resulting in very long acquisition times. GQI (Fang-Cheng Yeh et al.) is able to resolve crossing fibres using as little as 101 directions.

37. GQI imaging parameters Acquisition time: 14mins, 21 secs 55 slices (full brain coverage) resolution: 2.5x2.5x2.5mm 3 101 directions Maximum b-value: 4000 s/mm 2 TE: 69ms TR=8200ms

38. GQI tractography GQI is able to identify multiple fibre crossings in numerous places in the brain. Small bundles such as the arcuate, the fornix, the uncinate can be seen very clearly and in great detail. Analysis done with Dipy http://nipy.sourceforge.net/dipy Eleftherios Garyfallidis

39. GQI – FA results Marta Correia ***

40. Magnetization Transfer Imaging

41. Magnetization Transfer Imaging (MTI) MT contrast occurs when there is fast exchange between bound and free protons. Bound or restricted protons are the ones associated with macromolecules or hydration layers. This restricted pool has a very short T2 and are invisible at the TEs used for standard MR imaging. However it can influence the observed MR signal through the exchange of energy (magnetization) between the two pools. M 0A M 0B R A B RARA RBRB

42. Magnetization Transfer Imaging (MTI) The bound pool has a broader excitation profile This pool can be excited by an RF pulse at a frequency several KHz away from the free water resonance frequency Exchange of protons between the two pools means that saturated magnetization from the bound pool will move into the liquid pool The total MR signal that can be observed decreases.

43. Magnetization Transfer Ratio (MTR) - = Baseline image (PD weighted) Magnetization weighted image Magnetization transfer ratio (MTR)

44. Magnetization Transfer Ratio (MTR) The myelin molecules present in white matter result in a very significant signal decrease when MT contrast is applied. MTR can be used as a measure of myelination. MTR has application in MS, ageing, schizophrenia, TBI and others.

45. MTI imaging parameters Acquisition time: 2x 2mins 36 sec (5 min 12 secs) 84 slices (full brain coverage) in-plane resolution: 1.5x1.5mm 2 Slice thickness: 1.5mm (no gap) TR=30ms TE=5ms

46. Susceptibility Weighted Imaging

47. Susceptibility weighted imaging (SWI) This method exploits the susceptibility differences between tissues. Magnitude and phase data are combined to produce an enhanced contrast magnitude image which is very sensitive to venous blood, hemorrhage and iron storage. Applications in the study of TBI, stroke and hemorrhage, tumours, MS and others.

48. SWI imaging parameters Acquisition time: 6mins 28 secs 72 slices in-plane resolution: 0.6x0.5mm 2 Slice thickness: 1.2mm (no gaps) TR: 28ms TE: 20ms

49. Thank you Rhodri Cusack Stefan Hetzer Annika Linke Eleftherios Garyfallidis Jason Taylor Michele Veldman Lorina Naci Jonathan Peelle Matt Davis Rik Henson Steve, Helen and Di Everybody who has volunteered as subjects.

50. And that’s all! For now...