Hankyeol Lee1, Rüdiger Stirnberg2, Tony Stöcker2,3, and Kâmil Uludağ1,4,5
1Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, Republic of Korea, 2German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany, 3Department of Physics and Astronomy, University of Bonn, Bonn, Germany, 4Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Korea, Republic of, 5Techna Institute & Koerner Scientist in MR Imaging, University Health Network, Toronto, ON, Canada
Synopsis
This study
presents the performance of 2D and 3D EPI sequences at 7T for functional
imaging. Eleven subjects were scanned with individually optimized 2D and 3D EPI
sequences with TR and total parallel imaging acceleration that were matched. Three
spatial resolutions: 0.8 mm, 1.1 mm, and 1.7 mm isotropic, were used. Resulting
temporal signal-to-noise ratios (tSNR) were compared between 2D and 3D EPI
sequences, and their potential functional sensitivities are discussed. The
results show images acquired with 3D EPI have higher tSNR at 0.8 mm and 1.1 mm
resolutions, while 2D EPI images have higher tSNR at 1.7 mm resolution.
Introduction
Ultra-high-field
(UHF) MRI scanners enable functional imaging at very high spatial resolutions (<1 mm3), allowing to probe the mesoscopic organization of human brain
function. Previous studies have suggested that 3D EPI sequences are capable of outperforming 2D EPI in functional imaging, when operated under thermal rather than physiological
noise-dominated regime.1-3 In
such cases, temporal signal-to-noise ratio (tSNR) and capturing event-related
effects in brain can be enhanced. This study examines spatial and temporal
properties of 2D and 3D EPI sequences at 7T scanner with different
spatial resolutions (0.8 mm, 1.1 mm, and 1.7 mm isotropic).Methods
Data Acquisition
All experiments
were conducted using a 7T whole-body scanner (Magnetom Terra, Siemens
Healthineers, Erlangen, Germany) and a 32-Rx/1-Tx head coil (Nova Medical,
Wilmington, MA, USA). Eleven healthy subjects were scanned pursuant to the
procedures approved by the institutional review board. Their written consents
were collected prior to scanning.
Two
sessions of task-based fMRI experiments with visual stimulation were performed
for nine subjects. Vendor-provided 2D EPI sequence and a custom 3D EPI sequence
developed by Stirnberg, et al. (2017) were used with three spatial resolutions
(0.8/1.1/1.7 mm isotropic).4 Whole-brain
coverage was obtained at 1.1 mm and 1.7 mm resolutions (number of slices = 112)
while partial-brain volumes were acquired with 0.8 mm resolution (number of
slices = 64). Scanning parameters were optimized for each sequence and
resolution. Flip angles for 2D and 3D sequences were 75-degrees and
14-degrees, respectively. For both 2D and 3D EPI, 3×2
(in-plane x slice) acceleration was used (FOV/3 shift and CAIPI shift 1,
respectively). All TRvol were matched to 3.2
seconds. TE for 1.1 mm and 1.7 mm resolutions were set to 19 ms for both 2D and
3D EPI. However, at 0.8 mm resolution, TEs were set to minimum achievable
values, which were 29 ms and 21 ms for 2D and 3D EPI, respectively.
A
flickering checkerboard pattern with 6.25 Hz frequency in blocks of 19.2/41.6 s
on/off was used for visual stimulation. Additional resting state images with
same protocols were acquired from two other subjects. Total 89 volumes were
acquired for each run.
Data Analysis
FSL tools,
including MCFLIRT, BET and FLIRT (version 6.0, FMRIB Software Library, Oxford,
UK), were used to apply motion correction and to linearly register images that
were acquired with 2D and 3D EPI.5-7 After
applying motion correction and brain extraction, six volumes prior to each
stimulation period and the last six volumes of each run were extracted for calculating tSNR. Additionally, percent difference in tSNR
comparing 3D to 2D EPI images was calculated for each resolution per subject:
$$\textrm{percent difference}=\frac{tSNR_{3D}-tSNR_{2D}}{tSNR_{2D}}*100\%$$
FMRI
data with visual task were processed using FEAT. No Gaussian smoothing was
applied and Z-statistic images were thresholded with Z>3.0 and P<0.05.Results and Discussion
Figure 1 displays tSNR and noise maps of a subject’s brain during
a single session. Images
acquired with 3D EPI at 0.8 mm and 1.1 mm resolutions had greater tSNR than 2D
EPI images. However, 3D EPI at 1.7 mm resolution had more noise than 2D EPI
images, heavily affected by its known characteristic of capturing greater
amount physiological noise than 2D sequences.1 Table 1 illustrates
tSNR comparison between spatial resolutions averaged per subject. One
subject’s data were excluded due to severe artifacts along the slice direction
in 2D EPI images.
In addition, Figure 2 illustrates percent differences in tSNR
between 2D and 3D EPI images from one subject. Overall tSNR was higher for 3D
EPI at 0.8 mm resolution. At 1.1 mm, evidently higher tSNR for 3D EPI was
observed for most of the displayed slice. However, 3D EPI had lower tSNR in the
occipital lobe. This may be due to 3D EPI’s more disadvantageous g-factor
penalty or particularly strong physiological artifacts in this area, given that
low flip angles were used in 3D EPI compared to 2D EPI. At 1.7 mm, 2D EPI had
overall dominance in tSNR. For the presented comparison, 2D and 3D
EPI protocols were individually optimized (e.g. FLEET8 vs. FLASH autocalibration9, fat saturation vs. binomial water excitation10). On the other hand, TR was adjusted according to the more time-limited
2D EPI (longer multiband pulses and fat saturation per TR). In particular with
elliptical sampling, 3D EPI could be considerably faster without changing
parallel imaging.4 Future analysis including physiological noise
correction is expected to produce higher tSNR and z-scores for both sequences. This will give stronger
boost to 3D EPI, particularly at lower spatial and
temporal resolutions.4,11 Conclusion
This study provides evidence that 3D EPI sequence has the capacity to outperform 2D EPI in high-resolution fMRI. Images acquired with three isotropic spatial resolutions (0.8 mm, 1.1 mm, and 1.7 mm) across eleven subjects showed different levels of tSNR. While 3D EPI at 0.8 mm and 1.1 mm resolutions yielded greater tSNR compared to 2D EPI, the same was not true at 1.7 mm resolution. This is likely due to 3D EPI’s greater susceptibility to physiological noise, which, however, can be corrected using various methods.1,12 Functional sensitivity evaluation of EPI sequences is ongoing. For illustrative purposes, Figure 3 shows different levels of activation in the occipital lobe of one subject, arranged by pulse sequences and spatial resolutions.Acknowledgements
This work was supported by the Institute for Basic Science under grant IBS-R015-D1.References
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