An T. Vu1,2, Alex Beckett1, Kawin Setompop3, and David A. Feinberg1,2
1Helen Wills Neuroscience Institute, UC Berkeley, Berkeley, CA, United States, 2Advanced MRI Technologies, Sebastopol, CA, United States, 3Martinos Center for Biomedical Imaging, Charlestown, MA, United States
Synopsis
We evaluate the
synergistic combination of super-resolution and SMS for high-resolution
whole brain fMRI. We find that SLIDER-SMS can acquire high resolution,
high CNR fMRI data at 3T which is normally only acquired at 7T. The regularized
deblurring/reconstruction of SLIDER yielded 40% more BOLD CNR than normally
acquired high resolution (HR) data, while omitting the deblurring step
altogether yielded 100% more BOLD contrast with similar high k-space frequency
tSNR. Future use of SLIDER for fMRI may enable robust columnar level results at
3T and allow higher spatial resolution fMRI investigations at 7T than currently
possible.Purpose
High isotropic resolution fMRI is challenging primarily due to
low SNR, especially at lower field strengths. Recently, Simultaneous
Multi-Slice (SMS) imaging with blipped-CAIPI (1, 2) has reduced scan time and improved SNR efficiency of fMRI. Similarly, super-resolution
techniques (3, 4) utilizing sub-voxel spatial shifts in the slice direction,
have increased both resolution and SNR efficiency.
Super-resolution techniques like SLIDER (2) may be particularly promising for
fMRI given that the thicker slices employed should enhance sensitivity to BOLD
susceptibility changes. Here we evaluate the synergistic combination of
super-resolution and SMS for high-resolution whole brain fMRI. Specifically: 1)
How does SLIDER fMRI compare to normally acquired high-resolution fMRI data
with and without post-processing blurring? 2) How does BOLD CNR and effective resolution
(i.e. residual blurring) vary as a function of deblurring regularization
parameter λ?
Methods
Data were acquired in three healthy volunteers on a Siemens 3T
Trio using a 32 ch head array. During the 2D gradient echo EPI fMRI scans,
subjects viewed 3 x 96 sec runs of flashing checkerboard (30 sec period)
stimulus per MB-5 (“High res”) and SLIDER-2 MB-5 protocols. Imaging parameters
were: 1.25 mm iso (nominal; 2.5 mm excitation thickness for SLIDER-2); FOV =
210x210x137.5 mm; PF = 6/8; TE = 45 ms; TR = 3000 ms (1500 ms per dithered
volume); Flip angle = 84
o (72
o for SLIDER-2); PE direction= AP; axial oblique
slices; and no in-plane undersampling. As a “High res blurred” control, the
MB-5 (“High res”) data were 2-slice window averaged. For
deblurring/reconstruction, the Toeplitz matrix was used as the forward model
(T) and Tickhnov regularization was used to calculate the inverse model (Tinv)
with λ ranging from 0 to 50% of the largest eigenvalue of T. In Matlab: Tinv =
(V*S/(S*S+eye(size(S))*max(diag(S))*λ)*U'); where [U S V] = svd(T). Note larger
λ’s result in greater residual blurring.
Results
Fig 1 shows the coronal cross section (of axially acquired
slices) of a representative subject’s “High res” (HR), “High res blurred”
(HRb), and SLIDER data deblurred with various λ values. Since HRb was blurred
in post processing, the original HR image is recovered perfectly without
regularization (λ=0). However, as with most super-resolution techniques in the
presence of noise, deblurring SLIDER without regularization results in high
spatial frequency noise amplification artifacts. SLIDER achieves best results with
modest regularization (λ~0.1). Fig 2 shows BOLD CNR (t-values) for the
corresponding Fig 1 datasets. SLIDER yields substantially stronger BOLD CNR
than HR and HRb. The amount of slice blur as a function of λ is plotted in Fig
3 left (quantified as the spatial correlation of the averaged time series with
that of the same image but shifted one slice down). The black vertical line
denotes the λ (~0.08) where the effective SLIDER slice resolution matches that
of HR. Error bars are SEM across subjects. The mean t-value as a function of λ
is shown in Fig 3 right. HRb has the expected sqrt(2) increase over HR. SLIDER
with λ~0.08 results in t-values at the level HRb. Without deblurring, SLIDER
results in over double the t-values as HR. Given that the slice blur metric of
Fig 3 may only be reflecting enhanced low relative to high spatial frequency
information, we also calculated the average k-space tSNR in the lowest 50%,
middle 25%, and highest 25% slice-axis k-space frequency regions (relative to
the low k-space region of HR; Fig 4 left). Notably, SLIDER without deblurring,
has significantly higher tSNR (p<0.05, paired-T(2)) in both low and mid
k-space frequencies and similar high k-space tSNR compared to HR and HRb (Fig 4
right). This shows that the SNR benefits of thick slice excitation in SLIDER
can offset the relative dampening of higher spatial frequencies. This is
critical, as prior literature has shown that with high CNR, even methods with
moderate amounts of blurring (e.g. in the PE direction due to T2* decay) can
yield maps of columnar level structure (5). Fig. 5 shows preliminary results
for 0.65 mm resolution ocular dominance mapping at 3T.
Conclusions
We find that SLIDER-SMS can acquire high resolution, high CNR
fMRI data at 3T which is normally only acquired at 7T. The BOLD CNR of SLIDER
was significantly greater than that of HR and even HRb due to the linear
relationship between voxel volume and SNR (as opposed to square root when
blurring in post processing) and the greater BOLD sensitivity with thicker
slices. Future use of SLIDER for fMRI may enable robust columnar level results
at 3T and allow higher spatial resolution fMRI investigations at 7T than
currently possible.
Acknowledgements
NIH BRAIN Initiative grant - 1R24MH106096References
1. Setsompop
K. et al, NI 2012 2. Chen, Vu et al,
NI 2015 3. Greenspan, H. et al, MRM 2002 4. Setsompop, K. et al,
ISMRM 2015 5. Yacoub et al, PNAS 2008 6. Cheng, Waggoner, and Tanaka, Neuron 2001.