1. fMRI: Biological Basis and Experiment Design Lecture 8: Pulse sequences, Take 2 Gradient echo review K-space review Slice selection K-space navigation –Bandwidth –Echo time –Read-out time

2. The read-out signal is the 1D FFT of the sample G RO --  0 Real part of signal in RF coil Magnitude of signal in RF coil Imaginary component of signal in RF coil

3. Pulse sequence diagram: slow 2D FLASH (64 x 64) N rep = 64 64 points RF G SS G PE G RO DAC PE table increments each repetition Flip angle ~ 56 deg. TR ~ 640us

4. Slice selection G = 5.1kHz/cm f x RF Pulse (bandwidth = 1kHz) Excited slice thickness = BW RF /G = 0.2cm = 2mm

5. Slice selection - edges aren’t exactly hard G = 5.1kHz/cm f x Frequency profile of pulse = spatial profile of slice BWthk = BW/G SS

6. Slice thickness is determined by bandwidth of pulse Slice position is determined by center frequency of pulse f x

7. Overlap of slices leads to non-uniform signal intensity for first few TRs f x 1 st TR30 th TR

8. Pulse sequence diagram: normal 2D FLASH (256 2 ) N rep = 256 256 points RF G SS G PE G RO DAC PE table increments each repetition Flip angle ~ 7 deg. TR ~ 10ms TE ~ 5ms

9. Pulse sequence diagram: normal 2D FLASH (256 2 ) N rep = 256 256 points RF G SS G PE G RO DAC PE table increments each repetition Flip angle ~ 7 deg. TR ~ 10ms TE ~ 5ms Read gradient amplitude, G RO : 35mT/m Dwell time (per data point): 3.5  s Sampling rate (bandwidth): 286kHz FOV = 286kHz/(1.49MHz/m) = 19.2cm N RO = 256 T RO (line) = 256*3.5us = 0.9ms Resolution = FOV RO /NR O = 0.75mm Frequency resolution (Hz/pixel) RO: 1.1kHz/px PE: effectively infinite TE = 5ms

10. FLASH sequences read one line per excitation --  0 Relative phase of spins

11. EPI sequences zig-zag back and forth across k-space --  0

12. Pulse sequence diagram: EPI (64 x 64 image) N rep = 32 64 pts RF G SS G PE G RO DAC 64 pts

13. Pulse sequence diagram: EPI (64 x 64 image) 64 RF G SS G PE G RO DAC 64 … … Read gradient amplitude, G RO : 35mT/m Dwell time (per data point): 3.5  s Sampling rate (bandwidth): 286kHz FOV = 286kHz/(1.49MHz/m) = 19.2cm N RO = 64 T RO (line) = 64*3.5us = 0.224ms T RO (image) = 64*64*3.5us = 14.3ms Resolution = FOV RO /NR O = 3.0mm Frequency resolution (Hz/pixel) RO: 4.5kHz/px (1/T RO,line ) PE: 70 Hz/px (1/T RO,image ) TE min = T RO /2 + fudge = 9ms

14. Pulse sequence diagram: EPI (more realistic) 64 RF G SS G PE G RO DAC 64 … … Read gradient amplitude, G RO : 15mT/m Dwell time (per data point): 8.1  s Sampling rate (bandwidth): 122kHz FOV = 122kHz/(0.64MHz/m) = 19.2cm N RO = 64 T RO (line) = 64*8.1us = 0.518ms T RO (image) = 64*64*3.5us = 33ms Resolution = FOV RO /NR O = 3.0mm Frequency resolution (Hz/pixel) RO: 1.9 kHz/px (1/T RO,line ) PE: 30 Hz/px (1/T RO,image ) TE min = T RO /2 + fudge = 18ms

15. A 3D object has a 3D k-space

16. Pulse sequence: 3D FLASH (176 x 224 x 256) N rep = 176 x 224 256 points RF G SS G PE G RO DAC PE table increments each repetition; cycles for each partition Slab is selected with very weak gradient Partition Encoding increments every 224 repetitions kxkx kyky kzkz