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Alexander D. Cohen

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YNIMG Journal 2021 Journal Article

Improved resting state functional connectivity sensitivity and reproducibility using a multiband multi-echo acquisition

Alexander D. Cohen
Baolian Yang
Brice Fernandez
Suchandrima Banerjee
Yang Wang

Recent advances in functional MRI techniques include multiband (MB) imaging and multi-echo (ME) imaging. In MB imaging multiple slices are acquired simultaneously leading to significant increases in temporal and spatial resolution. Multi-echo imaging enables multiple echoes to be acquired in one shot, where the ME images can be used to denoise the BOLD time series and increase BOLD sensitivity. In this study, resting state fMRI (rs-fMRI) data were collected using a combined MBME sequence and compared to an MB single echo sequence. In total, 29 subjects were imaged, and 18 of them returned within two weeks for repeat imaging. Participants underwent one MBME scan with three echoes and one MB scan with one echo. Both datasets were processed using standard denoising and advanced denoising. Advanced denoising included multi-echo independent component analysis (ME-ICA) for the MBME data and ICA-AROMA for the MB data. Resting state functional connectivity (RSFC) was evaluated using both selective seed-based and whole grey matter (GM) region-of-interest (ROI) based approaches. The reproducibility of connectivity metrics was also analyzed in the repeat subjects. In addition, functional connectivity density (FCD), a data-driven approach that counts the number of significant connections, both within a local cluster and globally, with each voxel was analyzed. Regardless of the standard or advanced denoising technique, all seed-based RSFC was significantly higher for MBME compared to MB. Much more GM ROI combinations showed significantly higher RSFC for MBME vs. MB. Reproducibility, evaluated using the dice coefficient was significantly higher for MBME relative to MB data. Finally, FCD was also higher for MBME vs. MB data. This study showed higher RSFC for MBME vs. MB data using selected seed-based, whole GM ROI-based, and data-driven approaches. Reproducibility found also higher for MBME data. Taken together, these results indicate that MBME is a promising technique for rs-fMRI.

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YNIMG Journal 2021 Journal Article

Using multiband multi-echo imaging to improve the robustness and repeatability of co-activation pattern analysis for dynamic functional connectivity

Alexander D. Cohen
Catie Chang
Yang Wang

Emerging evidence has shown that functional connectivity is dynamic and changes over the course of a scan. Furthermore, connectivity patterns can arise from short periods of co-activation on the order of seconds. Recently, a dynamic co-activation patterns (CAPs) analysis was introduced to examine the co-activation of voxels resulting from individual timepoints. The goal of this study was to apply CAPs analysis on resting state fMRI data collected using an advanced multiband multi-echo (MBME) sequence, in comparison with a multiband (MB) sequence with a single echo. Data from 28 healthy control subjects were examined. Subjects underwent two resting state scans, one MBME and one MB, and 19 subjects returned within two weeks for a repeat scan session. Data preprocessing included advanced denoising namely multi-echo independent component analysis (ME-ICA) for the MBME data and an ICA-based strategy for Automatic Removal of Motion Artifacts (ICA-AROMA) for the MB data. The CAPs analysis was conducted using the newly published TbCAPs toolbox. CAPs were extracted using both seed-based and seed-free approaches. Timepoints were clustered using k-means clustering. The following metrics were compared between MBME and MB datasets: mean activation in each CAP, the spatial correlation and mean squared error (MSE) between each timepoint and the centroid CAP it was assigned to, within-dataset variance across timepoints assigned to the same CAP, and the between-session spatial correlation of each CAP. Co-activation was heightened for MBME data for the majority of CAPs. Spatial correlation and MSE between each timepoint and its assigned centroid CAP were higher and lower respectively for MBME data. The within-dataset variance was also lower for MBME data. Finally, the between-session spatial correlation was higher for MBME data. Overall, our findings suggest that the advanced MBME sequence is a promising avenue for the measurement of dynamic co-activation patterns by increasing the robustness and reproducibility of the CAPs.

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