UCSF Hyperpolarized MR Seminar Summer 2019, Lecture #7 "EPI data processing" Lecturer: Adam Autry Sponsored by the NIH/NIBIB-supported UCSF Hyperpolarized MRI Technology Resource Center (P41EB013598) https://radiology.ucsf.edu/research/labs/hyperpolarized-mri-tech

1. Using EPI to investigate HP [1-13C]pyruvate
metabolism in glioma patients and healthy
volunteers
Adam W Autry, Jeremy W Gordon, Hsin-Yu Chen, Daniele
Mammoli, Marisa LaFontaine, Javier Villanueva-Meyer, Susan M
Chang, Duan Xu, Peder EZ Larson, Daniel B Vigneron,
Sarah J Nelson, and Yan Li
University of California, San Francisco (UCSF)

2. [1] Park et al, MRM 2018, [2] Miloushev et al, Cancer Res. 2018
Hyperpolarized (HP) 13C Imaging
Chemical shift (ppm)
190 185 180 175 170 165 160
pyruvate

3. Dynamic Echo Planar Imaging (EPI)
[3] Gordon et al, MRM, 2019
SPSP excitation
RF
Gz
Gy
Gx
TR/TE = 62.5 ms / 21.7ms
Spatial resolution = 2.88 – 8 cm3
Temporal resolution: 3s
13Cspectra
Chemical shift (ppm)
185 180 175 170 165 160
HP-13CEPI
pyruvate
𝛼=20∘
lactate
𝛼=30∘
bicarb
𝛼=30∘

4. Dynamic frequency-selective 13C EPI
Pyr
Lac
Bic
T1w

5. 2D multi-slice EPI
Noise-only data
Nyquist Ghost
Correction
Prewhitening Recon
1
ky/Echo#
Uncorrected Corrected
2
3
4
5
6
7
8
Noise Covariance Matrix
8
7
6
5
4
3
2
1
1 2 3 4 5 6 7 8ch
Channel
EPI Processing Framework

6. Coil Combination
Voxel-wise
phasing
AUC Images /
kPL, kPB Estimation
Combined Pyr
ch1
ch3
ch4
ch5
ch6ch7
ch8
AUC
Pyruvate
AUC
Lactate
AUC
Bicarb
0.036
0.018
0
ch2
kPL(sec-1)

7. Optimal Weights Coil Combination
𝑰 𝒎𝒆𝒕,𝒅𝒚𝒏 𝒙, 𝒚, 𝒄𝒐𝒊𝒍, 𝒔𝒍𝒊𝒄𝒆, 𝒇𝒓𝒂𝒎𝒆 % complex data after FFT
𝑰 𝒑𝒚𝒓 =
𝒇𝒓𝒂𝒎𝒆=𝟏
𝟐𝟎
𝑰 𝒑𝒚𝒓,𝒅𝒚𝒏 % temporally-summed RefPeak map
𝑰 𝒑𝒚𝒓,𝑺𝑶𝑺 =
𝒄𝒐𝒊𝒍=1
32
|𝑰 𝒑𝒚𝒓(𝒙, 𝒚, 𝒄𝒐𝒊𝒍, 𝒔𝒍𝒊𝒄𝒆)|2 % normalization factor for RefPeak map
𝒘𝒆𝒊𝒈𝒉𝒕 =
𝑰 𝒑𝒚𝒓
𝑰 𝒑𝒚𝒓,𝑺𝑶𝑺
% complex RefPeak coil weights
𝑰 𝒄𝒐𝒎𝒃 =
𝒄𝒐𝒊𝒍=𝟏
𝟑𝟐
𝒘𝒆𝒊𝒈𝒉𝒕∗ 𝒙, 𝒚, 𝒄𝒐𝒊𝒍, 𝒔𝒍𝒊𝒄𝒆 𝑰 𝒎𝒆𝒕,𝒅𝒚𝒏
% weighted-sum combination
% peformed for each frame

8. Voxel-wise Phasing
S = |𝑨𝑼𝑪𝒍𝒂𝒄|𝒆𝒊∡(𝑨𝑼𝑪 𝒑𝒚𝒓 𝑨𝑼𝑪𝒍𝒂𝒄
∗
)
𝚫𝝓 𝒑𝒚𝒓−𝒍𝒂𝒄 = −( ∡𝑺 )|𝑺|
𝑰𝒍𝒂𝒄,𝒑𝒉𝒂𝒔𝒆𝒅 = 𝑰𝒍𝒂𝒄,𝒅𝒚𝒏 𝒆−𝒊(∡𝑨𝑼𝑪 𝒑𝒚𝒓+𝚫𝝓 𝒑𝒚𝒓−𝒍𝒂𝒄)
𝑰 𝒑𝒚𝒓,𝒑𝒉𝒂𝒔𝒆𝒅 = 𝑰 𝒑𝒚𝒓,𝒅𝒚𝒏 𝒆−𝒊∡𝑨𝑼𝑪 𝒑𝒚𝒓
𝑰 𝒃𝒊𝒄,𝒑𝒉𝒂𝒔𝒆𝒅 = 𝑰 𝒃𝒊𝒄,𝒅𝒚𝒏 𝒆−𝒊∡𝑨𝑼𝑪 𝒃𝒊𝒄
% phase difference between pyr and lactate
% directly phase pyruvate (highest SNR)
% phase lactate relative to pyruvate
% directly phase bicarbonate to avoid flow
% affects from blood
% assume no temporal change in phase

9. Regions of Interest
NORMAL-APPEARING
WHITE MATTER
PUTATIVE TUMOR:
T2 LESIONT2LWM
REGIONS OF INTEREST
Normal-appearing
white matter (NAWM)
T2 Lesion (T2L)

10. Kinetic traces and fitting: NAWM
4
3
0
Post-injection time (s)
10 20 30 40 50 60
0
White matter traces
0
1
2
5
6
HP-13Csignal(AU)

11. kPL& kPB Maps with ROIs
0.03
0.015
0 kPL(s-1)
0.0104
0.0052
kPB(s-1)
0
White matter traces
6
)
[7] Crane et al, SIVIC visualization

12. Healthy Control
0
kPL(s-1)kPB(s-1)
0.028
0.014
0
0.0078
0.0039
B
A
0.022
32ch
Test / Re-Test kPL,NAWM : 0.017 ± 0.001 / 0.017 ± 0.002 s-1

13. Test 30-min Re-Test: Healthy Control0
kP
B
kPL(s-1)
0.022
0.011
0
Re-Test:24chTest:32ch
Test / Re-Test kPL,NAWM : 0.017 ± 0.001 / 0.017 ± 0.002 s-1

14. Serial HP Data
0.036+
kPL(s-1)
0.018
0
0.009
0.027
TP8+bevTP7+bevTP5TP6
0 10 20 30 40 50 0 10 20 30 40 50
Time (s) Time (s)
2000
4000
6000
8000
10000
2000
1000
3000
HP-13CSignal(AU)
Pyruvate
Lactate
Bicarbonate
Post-bevacizumabPre-bevacizumab
Recirculation
Normal-appearing white matter
Patient with glioma before and
during treatment with anti-
angiogenic agent bevacizumab