Comparison of SMS-EPI and 3D-EPI at 7T in an fMRI localizer study with matched spatiotemporal resolution and homogenized excitation profiles

Abstract

The simultaneous multi-slice EPI (SMS-EPI, a.k.a. MB-EPI) sequence has met immense popularity recently in functional neuroimaging. A still less common alternative is the use of 3D-EPI, which offers similar acceleration capabilities. The aim of this work was to compare the SMS-EPI and the 3D-EPI sequences in terms of sampling strategies for the detection of task-evoked activations at 7T using detection theory. To this end, the spatial and temporal resolutions of the sequences were matched (1.6 mm isotropic resolution, TR = 1200 ms) and their excitation profiles were homogenized by means of calibration-free parallel-transmission (Universal Pulses). We used a fast-event “localizer” paradigm of 5:20 min in order to probe sensorimotor functions (visual, auditory and motor tasks) as well as higher level functions (language comprehension, mental calculation), where results from a previous large-scale study at 3T (N = 81) served as ground-truth reference for the brain areas implicated in each cognitive function. In the current study, ten subjects were scanned while their activation maps were generated for each cognitive function with the GLM analysis. The SMS-EPI and 3D-EPI sequences were compared in terms of raw tSNR, t-score testing for the mean signal, activation strength and accuracy of the robust sensorimotor functions. To this end, the sensitivity and specificity of these contrasts were computed by comparing their activation maps to the reference brain areas obtained in the 3T study. Estimated flip angle distributions in the brain reported a normalized root mean square deviation from the target value below 10% for both sequences. The analysis of the t-score testing for the mean signal revealed temporal noise correlations, suggesting the use of this metric instead of the traditional tSNR for testing fMRI sequences. The SMS-EPI and 3D-EPI thereby yielded similar performance from a detection theory perspective.

The Dual Mechanisms of Cognitive Control dataset, a theoretically-guided within-subject task fMRI battery

“…Temporal signal to noise ratio (tSNR) images are calculated by dividing the mean by the standard deviation of all frames within a run in each voxel (or vertex), after preprocessing. While not isolating task signal, tSNR (as well as the temporal mean and standard deviation) images are valuable for identifying acquisition artifacts, areas of signal dropout, and relative differences across participants or runs (Inglis 2011a;2011b;Le Ster et al 2019;Welvaert and Rosseel 2013;De Blasi et al 2020). Figure 7 shows the median volumetric tSNR image.…”

“…To avoid circularity, control analyses must have high face validity, and be independent of experimental hypotheses. The use of positive control analyses is especially valuable in task fMRI datasets, given the lack of unambiguous methods for estimating the relevant contrast to noise ratio, or thresholds for motion or tSNR (Botvinik-Nezer et al 2019;De Blasi et al 2020;Welvaert and Rosseel 2013;Lutti et al 2013;Le Ster et al 2019). Currently, we use two positive control analyses for quality control, implemented as separate GLMs.…”

Ultra‐high spatial resolution BOLD fMRI in humans using combined segmented‐accelerated VFA‐FLEET with a recursive RF pulse design

“…85 It too is commonly used for high-resolution fMRI as it tends to have elevated tSNR relative to 2D-EPI when thermal noise dominated. [85][86][87][88][89] For fMRI sequences that are not in a steady-state due to a contrast preparation, like VAscular Space Occupancy 88 or ASL, 90 the recursive pulse design could improve the slab profile consistency when using 3D-EPI readouts. Note, since 3D-EPI uses the same readout trajectory per partition as 2D-EPI, it is subject to the same in-plane spatial encoding limitations discussed throughout.…”

Segmented K‐space blipped‐controlled aliasing in parallel imaging for high spatiotemporal resolution EPI

“…An increasing number of structural imaging, [1][2][3][4][5][6] quantitative imaging, [7][8][9][10] or high spatiotemporal resolution functional imaging [11][12][13][14][15][16][17][18][19][20][21] applications have been approached by dedicated EPI 22 implementations. Many of those aim at higher spatial resolution than usual, for example, in fMRI.…”