Synopsis
Phase encoded MR spectroscopic imaging
(MRSI) is a time-consuming protocol because there is a large number of phase
encodings to be collected. Non-uniform
undersampling (NUS) and Compressed Sensing (CS), which has been widely used in
MRI/MRS can be used to speed up the acquisition further. In this study, we have implemented a novel CS based multi -echo echo planar J-Resolved
spectroscopic imaging (ME-EP-JRESI) acquisition and CS reconstruction in in human brain at 3T. We were able to
detect and quantify several metabolites using a modified ProFit algorithm. The
CS reconstructed spectra were of high quality, with metabolite ratios matching
the fully encoded data closely.Purpose/Introduction:
Localized J-resolved spectroscopy (JPRESS), which resolve overlapping metabolites better than
1D MRS taking advantage of J-coupling interactions between protons of
metabolites and an extra spectral
dimension, has previously been shown to be a powerful tool in the study
of metabolism in human brain in vivo
1, 2. To increase the spatial
coverage, J-resolved spectroscopy sequence was modified with an echo-planar
spectroscopic imaging (EPSI)
3-5 readout to yield a novel
four-dimensional (4D) spectroscopic
imaging (SI) (2 spectral and 2 spatial) called echo-planar J –resolved
spectroscopic imaging (EP-JRESI)
6 that allows collection of 2D
JPRESS spectra from multiple regions in a single experiment. One of the
limitations of EP-JRESI to use in human brain is the long scan time. A
significant acceleration was achieved for the EP-JRESI using a multi-echo (ME) based
acquisition scheme, called Multi-Echo based Echo-Planar J-resolved Spectroscopic Imaging (ME-EP-JRESI)
7,
which uses two
bipolar echo-planar imaging (EPI) read-out trains to collect dual phase encoded
lines within a single TR
2. But acquisition duration still remains a
limitation for a routine clinical use in brain. Non-uniform
undersampling (NUS) and Compressed Sensing (CS)
8, which has been
widely used in MRI/MRS can be used to speed up ME-EP-JRESI acquisition further.
In this study, we have implemented a
novel CS based ME-EP-JRESI acquisition and CS reconstruction in human brain at 3T. We further quantify the
metabolites from prospectively undersampled brain phantom data using prior
knowledge fitting (ProFit) algorithm
9 to determine the
integrity and reproducibility of CS reconstruction.
Materials and Methods:
The basic 4D ME-EP-JRESI sequence (Fig. 1) which uses a 90°–180°-Δt1-180° scheme for localization was modified by imposing non-uniform sampling (2X) along the
t
1 direction using a exponential sampling density scheme. To examine the performance and
reliability, fully encoded phantom data were collected together with
prospectively undersampled phantom scans. The sequence was tested further in
the brain of five healthy volunteers (age=23-58 years).
All data were collected on a 3T Prisma MRI scanner with a 16-channel head
‘receive’ coils. The following parameters were used for both fully sampled and
NUS-based ME-EP-COSI phantom data: TR/TE=2s/30ms, 1x1x2cm
3 voxel
for VOI localization, 100 Δt
1 increments, 256 bipolar
echo pair, FOV=16x16cm
2, F
1 and F
2 bandwidths of 1000 Hz and 1190 Hz
respectively. A non-water-suppressed ME-EP-JRESI data with t
1=1 were
also recorded. In-vivo data were
collected using the same parameters as the phantom scans except that the TR was
decreased to 1.5s and t1 increments to 64 for a scan time ~7min. The
undersampled data was reconstructed using a modified Split Bregman algorithm
10
which solves the unconstrained optimization problem, $$$\arg min_{u}
\|\triangledown\ u\|_1 +\frac{\lambda}{2} \|F_{p}u - d\|_2^2$$$ where u is
the reconstructed data, ∇ is
the gradient operator,
Fp is the undersampled Fourier
transform,
d is the under-sampled data, λ is a regularization parameter,
and
||x||n is the l
n norm. Acquired data were
post-processed with a custom MATLAB-based library and then reconstructed using
CS along the t
1 dimension. Modified version of the Profit algorithm was used
for quantitation and metabolite ratios were calculated with respect to the 3.0
ppm creatine peak (S/SCr).
Results
and Discussion:
Figure 2(a) shows the PRESS VOI localization volume on
a T1-weighted axial MRI of a 38-year-old healthy subject brain.
Spatial distribution of Cr/Cho map from the same subjects is shown in Figure
2(b) and representative 2D J-resolved spectra extracted from the left
hippocampus and thalamus regions following CS reconstruction are shown in
Figure 2(c) and 2(d) respectively. No visible aliasing is seen after the
reconstruction. All major metabolites: mI, creatine Cr, Cho, Glx, NAA are visible. Figure 3 shows the metabolite map of the 2D diagonal peaks
of Cr/Cho, and NAA from fully sampled and CS reconstructed ME-EP-JRESI phantom data.
The reconstructed metabolite map of the
diagonal peaks exhibited similar spatial profiles as that of the fully sampled
for 2x accelerations showing that the CS reconstruction successfully
cleans up the incoherent aliasing produced by the NUS. Figure 4 shows a
comparison of metabolite ratios with respect to Cr calculated by ProFit for the
fully-sampled, and prospectively 2x accelerated phantom datasets for the
central 4x4 voxels. The CS reconstructed spectra were of high quality, with
metabolite ratios matching the fully encoded data closely. Figure 5 shows extracted spectra from the same location for a fully
sampled and CS-reconstructed ME-EP-JRESI phantom data exhibiting similar
spectral profiles.
Conclusion:
This is an exploratory, validation, and feasibility
study for CS-based ME-EP-JRESI for human brain application at 3T. We have shown
that NUS/CS can successfully be applied to the ME-EP-JRESI sequence providing
an acceleration factor of 2x. All these bring ME-EP-JRESI closer to becoming a
clinical reality.
Acknowledgements
This
research was supported by National Institute of Health (NIH) grant 1R21NS08064901A1.References
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