Quantifying the Statistical Impact of GRAPPA in fcMRI Data With a Real-Valued Isomorphism

Bruce, Iain P.; Rowe, Daniel B.

doi:10.1109/tmi.2013.2288521

Cited by 6 publications

(5 citation statements)

References 37 publications

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“…The blue arrows in the sagittal and coronal views are located at (63,44,54) and (63,44,27) in the scanner coordinate system, and these locations are aliased in the AF = 8 and FOV/3 acquisition protocol for both LR and RL encoding. The brown arrows in the coronal view are examples of aliased locations (7,44,57) and (7,44,30) in which the source of the signal is uncertain; they are close to but not contained in the LR aliased regions of the motor cortex (white) (nor are they contained in RL aliased locations). Thresholded at > 1.96.…”

Section: Slice Leakagementioning

confidence: 99%

“…The questions and insights raised by Todd et al (2016) in part motivated our investigation of the patterns of regional aliasing and a formal evaluation of the statistical impacts of SMS acquisition including the impacts of smoothing. The impacts of signal leakage have been demonstrated for in-plane acceleration, where interpolation using the in-plane GRAPPA kernel and spatial smoothing induce correlations between aliased and neighboring voxels (Bruce and Rowe, 2014). Here, we characterize signal leakage due to slice leakage, which causes signal to leak into distant voxels, and smoothing leakage, which is associated with signal leaking into neighboring voxels.…”

Section: Introductionmentioning

confidence: 97%

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Impacts of simultaneous multislice acquisition on sensitivity and specificity in fMRI

2018

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Simultaneous multislice (SMS) imaging can be used to decrease the time between acquisition of fMRI volumes, which can increase sensitivity by facilitating the removal of higher-frequency artifacts and boosting effective sample size. The technique requires an additional processing step in which the slices are separated, or unaliased, to recover the whole brain volume. However, this may result in signal "leakage" between aliased locations, i.e., slice "leakage," and lead to spurious activation (decreased specificity). SMS can also lead to noise amplification, which can reduce the benefits of decreased repetition time. In this study, we evaluate the original slice-GRAPPA (no leak block) reconstruction algorithm and acceleration factor (AF = 8) used in the fMRI data in the young adult Human Connectome Project (HCP). We also evaluate split slice-GRAPPA (leak block), which can reduce slice leakage. We use simulations to disentangle higher test statistics into true positives (sensitivity) and false positives (decreased specificity). Slice leakage was greatly decreased by split slice-GRAPPA. Noise amplification was decreased by using moderate acceleration factors (AF = 4). We examined slice leakage in unprocessed fMRI motor task data from the HCP. When data were smoothed, we found evidence of slice leakage in some, but not all, subjects. We also found evidence of SMS noise amplification in unprocessed task and processed resting-state HCP data.

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Section: Slice Leakagementioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

Impacts of simultaneous multislice acquisition on sensitivity and specificity in fMRI

2018

Self Cite

View full text Add to dashboard Cite

show abstract

“…The questions and insights raised by in part motivated our investigation of the patterns of regional aliasing and a formal evaluation of the statistical impacts of SMS acquisition including the impacts of smoothing. The impacts of signal leakage have been demonstrated for in-plane acceleration, where interpolation using the in-plane GRAPPA kernel and spatial smoothing induce correlations between aliased and neighboring voxels (Bruce and Rowe, 2014). Here, we characterize signal leakage due to slice leakage, which causes signal to leak into distant voxels, and smoothing leakage, which is associated with signal leaking into neighboring voxels.…”

Section: Introductionmentioning

confidence: 97%

Impacts of Simultaneous Multislice Acquisition on Sensitivity and Specificity in fMRI

Risk

Kociuba

Rowe

2018

Preprint

Self Cite

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Simultaneous multislice (SMS) acquisition can be used to decrease the time between acquisition of fMRI volumes, which can increase sensitivity by facilitating the removal of higherfrequency artifacts and boosting effective sample size. The technique requires an additional processing step in which the slices are separated, or unaliased, to recover the whole brain volume. However, this may result in signal "leakage" between aliased locations, i.e., slice "leakage," and lead to spurious activation (decreased specificity). SMS can also lead to noise amplification, which can reduce the benefits of decreased repetition time. In this study, we evaluate the original slice-GRAPPA (no leak block) reconstruction algorithm and acquisition scenarios used in the young adult Human Connectome Project (HCP), as well as split slice-GRAPPA (leak block). In addition to slice leakage, signal leakage can result from spatial smoothing, i.e., smoothing leakage, which leads to inflated regions of activation. Previous studies have generally found that SMS acquisition results in higher test statistics and/or a greater number of activated voxels. Here, we use simulations to disentangle this phenomenon into true positives (sensitivity) and false positives (decreased specificity). Slice leakage was greatly decreased by split slice-GRAPPA. Noise amplification was decreased by using moderate acceleration factors (AF = 4). We examined slice leakage in unprocessed fMRI motor task data from the HCP, which used the original slice-GRAPPA. When data were smoothed, we found evidence of slice leakage in some, but not all, subjects. We also found evidence of SMS noise amplification in unprocessed task and processed resting-state HCP data.

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“…An earlier study by Bruce and Rowe investigated this problem in the context of functional MRI (fMRI). 10 They reported artificially induced correlations in voxel time courses in conventional GRAPPA reconstruction in single-band acquisitions for fMRI. Their goal was to highlight the false functional connectivity results in GRAPPA accelerated fMRI experiments.…”

mentioning

confidence: 99%

Analysis of errors in diffusion kurtosis imaging caused by slice crosstalk in simultaneous multi‐slice imaging

et al. 2019

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Simultaneous multi‐slice (SMS) imaging techniques accelerate diffusion MRI data acquisition. However, slice separation is imperfect and results in residual signal leakage between the simultaneously excited slices. The resulting consistent bias may adversely affect diffusion model parameter estimation. Although this bias is usually small and might not affect the simplified diffusion tensor model significantly, higher order diffusion models such as kurtosis are likely to be more susceptible to such effects. In this work, two SMS reconstruction techniques and an alternative acquisition approach were tested to quantify the effects of slice crosstalk on diffusion kurtosis parameters. In reconstruction, two popular slice separation algorithms, slice GRAPPA and split‐slice GRAPPA, are evaluated to determine the effect of slice leakage on diffusion kurtosis metrics. For the alternative acquisition, the slice pairings were varied across diffusion weighted images such that the signal leakage does not come from the same overlapped slice for all diffusion encodings. Simulation results demonstrated the potential benefits of randomizing the slice pairings. However, various experimental factors confounded the advantages of slice pair randomization. In volunteer experiments, region‐of‐interest analyses found high metric errors with each of the SMS acquisitions and reconstructions in the brain white matter.

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Quantifying the Statistical Impact of GRAPPA in fcMRI Data With a Real-Valued Isomorphism

Cited by 6 publications

References 37 publications

Impacts of simultaneous multislice acquisition on sensitivity and specificity in fMRI

Impacts of simultaneous multislice acquisition on sensitivity and specificity in fMRI

Impacts of Simultaneous Multislice Acquisition on Sensitivity and Specificity in fMRI

Analysis of errors in diffusion kurtosis imaging caused by slice crosstalk in simultaneous multi‐slice imaging

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