1. fMRI: Biological Basis and Experiment Design Lecture 9: Pulse sequences, Take 3 Slice selection homework review Pulse sequence/k- space trajectory matching Spin echo http://www-mrsrl.stanford.edu/~brian/mri-movies/

2. Protons on water molcules: Ernst's "spies"  =  B =  B  = 267 x 10 6 (rad/s)/T  = 42.6 MHz/T

3. Slice selection - edges aren’t exactly hard f x Frequency profile of pulse = spatial profile of slice BWthk = BW/G SS G = 12 mT/m = 1.2 G/cm =  * x * G

4. Pulse sequence diagram: N rep = 256 256 points RF G SS G PE G RO DAC Flip angle = 7 deg. TR = 10ms TE ~ 5ms Sequence type: FLASH Contrast: T 1 Image resolution: 256 x 256 Total acquisition time: 256 x 10ms = 2.5s Sequence type: ___________ Contrast: ___________ Image resolution: ___________ Total acquisition time: ___________

5. K-space trajectory and scaled T 2 * decay in gray matter: 256 (complex-valued) points 1 2 3 4 256 … T acq = 2.5ms TE = 5ms time (ms) MM 256 lines

6. Image:

7. 64 RF G SS G PE G RO DAC 64 … … (64 times) Echo spacing = 0.57ms Pulse sequence diagram: Flip angle = 75 degrees Sequence type: EPI Contrast: T 1 and T 2 * Image resolution: 64 x 64 Image acq. time: 64 x 0.57ms = 36.48ms TR = 1.5 s TE = 30ms (32 nd line) Sequence type: ___________ Contrast: ___________ Image resolution: ___________ Image acq. time: ___________

8. K-space trajectory and scaled T 2 * decay in gray matter: 64 (complex-valued) points T acq = 35ms TE = 30ms time (ms) MM … 64 lines

9. Image: (resolution)(contrast)

10. 64 RF G SS G PE G RO DAC 64 … … (64 times) Echo spacing = 0.57ms Pulse sequence diagram: Flip angle = 75 degrees Sequence type: GE EPI Contrast: T 2 * Image resolution: 64 x 64 Image acq. time: 64 x 0.57ms = 36.48ms TR = 5 s TE = 30ms (32 nd line) Sequence type: ___________ Contrast: ___________ Image resolution: ___________ Image acq. time: ___________

11. K-space trajectory and scaled T 2 * decay in gray matter: 64 (complex-valued) points T acq = 35ms TE = 30ms time (ms) MM … 64 lines

12. Image: (resolution)(contrast)

13. 128 RF G SS G PE G RO DAC 128 … … (128 times) Echo spacing = 0.75ms Pulse sequence diagram: Flip angle = 90 degrees Sequence type: EPI Contrast: T 2 * Image resolution: 128 x 128 Image acq. time: 128 x 0.75ms = 96ms TR = 5 s TE = 55ms (65 th line) Sequence type: ___________ Contrast: ___________ Image resolution: ___________ Image acq. time: ___________

14. K-space trajectory and scaled T 2 * decay in gray matter: 128 (complex-valued) points T acq = 96 ms TE = 55 ms time (ms) MM … 128 lines

15. Image:

16. 128 RF G SS G PE G RO DAC 128 … … (96 times) Echo spacing = 0.75ms Pulse sequence diagram: Flip angle = 90 degrees Sequence type: EPI Contrast: T 2 * Image resolution: 128 x 128 Image acq. time: 96 x 0.75ms = 72 ms TR = 5 s TE = 30ms (32 nd line) Sequence type: ___________ Contrast: ___________ Image resolution: ___________ Image acq. time: ___________

17. K-space trajectory and scaled T 2 * decay in gray matter: 128 (complex-valued) points T acq = 72 ms TE = 30 ms time (ms) MM … 96 lines

18. Image:

19. Spin Echo 90 deg. 180 deg. time (ms) MM T2*T2* T2T2

20. 128 RF G SS G PE G RO DAC 128 … … (96 times) Echo spacing = 0.75ms Pulse sequence diagram: 90 deg. Sequence type: SE EPI Contrast: T 2 Image resolution: 128 x 128 Image acq. time: 96 x 0.75ms = 72 ms TR = 5 s TE = 60ms (32 nd line) 180 deg. Sequence type: ___________ Contrast: ___________ Image resolution: ___________ Image acq. time: ___________

21. K-space trajectory and scaled T 2 & T 2 * decay in gray matter: 128 (complex-valued) points T acq = 72 ms TE = 60 ms time (ms) MM … 96 lines 180  90  T2*T2* T2T2

22. Image:

23. 128 RF G SS G PE G RO DAC 128 … … (32 times) Echo spacing = 0.75ms Pulse sequence diagram: Flip angle = 40 degrees Sequence type: segmented EPI Contrast: T 1 and T 2 * Image resolution: 128 x 128 Segment acq. time: 32 x 0.75ms = 24 ms Image acq. time: 1 sec TE = 20ms (16 th line) N rep = 4 TR = 0.25 s Sequence type: ___________ Contrast: ___________ Image resolution: ___________ Segment acq. time: Image acq. time: ___________

24. K-space trajectory and scaled T 2 * decay in gray matter: 128 (complex-valued) points T acq,seg = 24ms TE = 20ms time (ms) MM … … … … 128 lines

25. Image: But not really... With the short read-out, the distortion would be much less noticeable. This acquisition had a short TE (using partial Fourier acquisition) but was not a segmented acquisition, so has more distortion than advertised.

26. RF G SS G PE G RO DAC … Echo spacing = 0.75ms Pulse sequence diagram: 90 deg. Sequence type: IR SE EPI Contrast: T 1 and (small amount of) T 2 Image resolution: 128 x 128 Image acq. time: 4 x 2.5s = 10 s TE = 25ms (16 th line) 180  N rep = 4 TR = 2.5 s TI = 0.9 s 180  … … … Sequence type: ___________ Contrast: ______________________ Image resolution: ___________ Image acq. time: ___________

27. K-space trajectory and scaled T 2 * decay in gray matter: 128 (complex-valued) points time (ms) MM … … … … 128 lines T acq,seg = 24ms TE = 40ms

28. Image:

29. Pulse sequence diagram: N rep = 176 x 224 256 points RF G SS G PE G RO DAC Sequence type: 3D FLASH Contrast: T 1 Image resolution: 256 x 224 x 176 Image acq. time: 176 x 224 x.01s = 6 min 34s Sequence type: ___________ Contrast: ______________________ Image resolution: ___________ Image acq. time: ___________ TR = 10ms

30. K-space trajectory and scaled T 2 * decay in gray matter: 256 (complex-valued) points T acq = 2.5ms TE = 5ms time (ms) MM 224 lines 176 partitions

31. Image: