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3D-UTE Rosette Applications (MRI and MRSI)
at UHF human (7T) and animal scanners
(9.4T) using The Berkeley Advanced
Reconstruction Toolbox (BART) toolbox
Uzay E Emir, Ali Ozen, Mark Chiew, Guy Williams, Zoe Kourtzi, Stephen Sawiak,
School of Health Sciences, Purdue University, West Lafayette, IN, United States
Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, United States,
Department of Radiology, Medical Center, University of Freiburg, Freiburg, Germany,
Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, United Kingdom
University of Cambridge, Wolfson Brain Imaging Centre, Cambridge, United Kingdom
University of Cambridge, The Adaptive Brain Lab, Cambridge, United Kingdom
A 3D-UTE Dual Echo Rosette MRI
and MRSI Sequence
2
Shen X, et al., doi: https://doi.org/10.1101/2021.09.18.460869
Normalized Radial UTE Reconstruction (RG) Normalized Rosette UTE Reconstruction (RG)
3D-UTE Rosette rocks
#5009
#1040
#1495 #1738
#1982 #5001 #1534
Day 1
Wednesday
Arrive at 3 pm: University of
Cambridge, Wolfson Brain Imaging
Centre, Cambridge, United
Kingdom
3:15 pm Installed the sequence
Of course, it did not work… 
Day 2 Thursday
• Arrive at 1 pm University of Cambridge, Wolfson Brain
Imaging Centre, Cambridge, United Kingdom
• Phantom Experiments
• Did it work?
• Of course, it did work…. How do I know?
The Berkeley Advanced
Reconstruction Toolbox
(BART) toolbox
• Problems
• Non-Cartesian K-space
trajectory
• Giant data size
• Limited computational power
• Solution
• The Berkeley Advanced
Reconstruction Toolbox
(BART) toolbox
Day 3 k-Space Design 3D Rosette (high-resolution)
• Siemen 7T Terra
• 32 Channel Nova Coil
• Kmax=500/m
• 𝜔1=𝜔2=0.766 kHz
• Field of view (FOV):240x240x240 mm3
• Matrix size=256x256x256,
• Readout dwell time=10 𝜇𝑠
• Flip angle=7-degree
• TR=7 ms,
• Readout duration=4.2 ms
• RF pulse duration=20 𝜇𝑠
• TE: 30 𝜇𝑠 and 2.12 ms
• Number of petals: 71442 (40%)
• Total scan time: 8.7 minutes
Sequential k-space fill-
in
Kz
(/m)
First Last
Reconstruction
Two reconstruction methods were performed: compressed sensing (as described above)
and regular regridding applying a density compensated (Pipe&Menon) adjoint NUFFT.
Adjouint NUFFT Total Reconstruction time: ~ 2 minutes
Compressed sensing ~10 minutes.
Day 3 ~ 1 mm isotropic Resolution 7T
~ 0.5 mm isotropic Resolution 7T
Day 3 How About 7T MRSI
• Siemen 7T Terra
• 32 Channel Nova Coil
• Field of view (FOV):240x240x240 mm3
• Matrix size=48x48x48,
• Readout dwell time=10 𝜇𝑠
• Flip angle=30-degree
• TR=500 ms,
• Readout duration=~460 us
• RF pulse duration=20 𝜇𝑠
• TE: 30 𝜇𝑠, Maximum
• Spectral Bandwidth ~4.4 Khz
• Number of petals: 1444
• Total scan time: ~10 minutes
How about 9.4T Bruker animal Scanner (PetalUTE, Stephen Sawiak)
3D-UTE Rosette rocks
#5009
#1040
#1495 #1738
#1982 #5001 #1534
Thank you so much

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3D-UTE Rosette MRI and MRSI at UHF human (7T) and animal scanners (9.4T) using The (BART) toolbox

  • 1. 3D-UTE Rosette Applications (MRI and MRSI) at UHF human (7T) and animal scanners (9.4T) using The Berkeley Advanced Reconstruction Toolbox (BART) toolbox Uzay E Emir, Ali Ozen, Mark Chiew, Guy Williams, Zoe Kourtzi, Stephen Sawiak, School of Health Sciences, Purdue University, West Lafayette, IN, United States Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, United States, Department of Radiology, Medical Center, University of Freiburg, Freiburg, Germany, Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, United Kingdom University of Cambridge, Wolfson Brain Imaging Centre, Cambridge, United Kingdom University of Cambridge, The Adaptive Brain Lab, Cambridge, United Kingdom
  • 2. A 3D-UTE Dual Echo Rosette MRI and MRSI Sequence 2 Shen X, et al., doi: https://doi.org/10.1101/2021.09.18.460869 Normalized Radial UTE Reconstruction (RG) Normalized Rosette UTE Reconstruction (RG)
  • 3. 3D-UTE Rosette rocks #5009 #1040 #1495 #1738 #1982 #5001 #1534
  • 4. Day 1 Wednesday Arrive at 3 pm: University of Cambridge, Wolfson Brain Imaging Centre, Cambridge, United Kingdom 3:15 pm Installed the sequence Of course, it did not work… 
  • 5. Day 2 Thursday • Arrive at 1 pm University of Cambridge, Wolfson Brain Imaging Centre, Cambridge, United Kingdom • Phantom Experiments • Did it work? • Of course, it did work…. How do I know?
  • 6. The Berkeley Advanced Reconstruction Toolbox (BART) toolbox • Problems • Non-Cartesian K-space trajectory • Giant data size • Limited computational power • Solution • The Berkeley Advanced Reconstruction Toolbox (BART) toolbox
  • 7. Day 3 k-Space Design 3D Rosette (high-resolution) • Siemen 7T Terra • 32 Channel Nova Coil • Kmax=500/m • 𝜔1=𝜔2=0.766 kHz • Field of view (FOV):240x240x240 mm3 • Matrix size=256x256x256, • Readout dwell time=10 𝜇𝑠 • Flip angle=7-degree • TR=7 ms, • Readout duration=4.2 ms • RF pulse duration=20 𝜇𝑠 • TE: 30 𝜇𝑠 and 2.12 ms • Number of petals: 71442 (40%) • Total scan time: 8.7 minutes Sequential k-space fill- in Kz (/m) First Last
  • 8. Reconstruction Two reconstruction methods were performed: compressed sensing (as described above) and regular regridding applying a density compensated (Pipe&Menon) adjoint NUFFT. Adjouint NUFFT Total Reconstruction time: ~ 2 minutes Compressed sensing ~10 minutes.
  • 9. Day 3 ~ 1 mm isotropic Resolution 7T ~ 0.5 mm isotropic Resolution 7T
  • 10. Day 3 How About 7T MRSI • Siemen 7T Terra • 32 Channel Nova Coil • Field of view (FOV):240x240x240 mm3 • Matrix size=48x48x48, • Readout dwell time=10 𝜇𝑠 • Flip angle=30-degree • TR=500 ms, • Readout duration=~460 us • RF pulse duration=20 𝜇𝑠 • TE: 30 𝜇𝑠, Maximum • Spectral Bandwidth ~4.4 Khz • Number of petals: 1444 • Total scan time: ~10 minutes
  • 11. How about 9.4T Bruker animal Scanner (PetalUTE, Stephen Sawiak)
  • 12. 3D-UTE Rosette rocks #5009 #1040 #1495 #1738 #1982 #5001 #1534
  • 13. Thank you so much

Editor's Notes

  1. With this in mind, we sought out to study the validity of a novel UTE 3D MRSI sequence with a rosette k-space trajectory for use in phosphorus-31 spectroscopic imaging. This sequence has been successfully tested in proton phantoms and phosphorus localization phantoms. The rosette trajectory’s multiple crossings of k-space origin theoretically lead to smooth transitions in temporal repetitions for spectra. Additionally, the unprecedently short UTE intrinsically avoids all baseline and phasing issues. More details can be found in the linked pre-printed paper below. To study this sequence, we recruited 5 healthy volunteers for uninterrupted, back-to-back leg muscle scanning with the novel MRSI sequence and an existing conventional MRSI sequence. We hypothesize that the novel UTE rosette sequence can simplify first-order phase and baseline corrections while providing competitive SNR relative to the conventional sequence.