Biology subjects

Brackenier, Y.

Publications and source records attributed to Brackenier, Y..

3 recordsLinked to original sources

bioRxiv2026

Scout-based Multi-Echo NAvigator (SMENA) for high temporal resolution motion and B0 estimation and correction: applications to multi-echo GRE and EPTI

PurposeTo develop a data-driven technique, Scout-based Multi-Echo NAvigator (SMENA), for joint estimation of motion and B0 inhomogeneity ({delta}B0) at a temporal resolution of [~]200 ms with minimal additional scan time for gradient-echo acquisition. MethodsSMENA consists of two key acquisition components: SMENA-scout and SMENA-nav. SMENA-scout is a rapid 3D 4-mm multi-echo acquisition completed in less than 8 seconds, providing images with matched contrast and phase at multiple echo times. SMENA-nav captures signal variations induced by motion and{delta} B0 during the scan using compact multi-echo navigator trajectories (3.5 ms) embedded within each TR. Motion and{delta} B0 maps were jointly estimated every [~]200 ms through a model-based optimization framework relating SMENA-scout to SMENA-nav. The estimation accuracy and correction performance of SMENA were evaluated in simulations and in vivo using multi-echo GRE and GRE-EPTI acquisitions. Multiple prospective motion experiments, including large continuous movement and deep breathing, were investigated. ResultsIn both simulations and in vivo experiments, accurate motion and{delta} B0 estimation were achieved. Compared with motion-only estimation, joint estimation reduced rotation and translation errors. Joint motion and{delta} B0 correction resulted in substantial improvements in image quality, particularly at longer echo times, producing an NRMSE of 10.4% compared to 31.6% with motion-only correction. High-temporal-resolution tracking of motion and{delta} B0 enabled improved reconstruction quality in scenarios involving continuous motion and deep breathing. ConclusionSMENA enables high-temporal-resolution joint estimation of motion and{delta} B0 with minimal additional acquisition cost, providing a practical solution for motion- and{delta} B0-robust MRI.

neuroscience↗

bioRxiv2024

Verifying the concordance between motion corrected and conventional MPRAGE for pediatric morphometric analysis

PurposeTo validate a retrospective motion correction technique, Distributed and Incoherent Sample Orders for Reconstruction Deblurring using Encoding Redundancy (DISORDER), for pediatric brain morphometry. MethodsTwo T1-weighted MPRAGE 3D datasets were acquired at 3T in thirty-seven children, median age 7.75 years; one with conventional linear phase encoding and one using DISORDER. MPRAGE images were scored as motion-free or motion-corrupt. Cortical morphometry and regional brain volumes were measured with FreeSurfer, subcortical grey matter (GM) with FSL-FIRST, and hippocampal volumes with HippUnfold. Intraclass correlation coefficient (ICC) was used to determine agreement between the 2 MPRAGE acquisitions. Mann-Whitney U was used to test the difference between measures obtained using DISORDER and (i) motion-free and (ii) motion-corrupt conventional MPRAGE data. ResultsICC measures were good/excellent for most subcortical GM (motion-free, 0.75-0.96; motion-corrupt, 0.62-0.98) and regional brain volumes (motion-free 0.47-0.99; motion-corrupt, 0.54-0.99) between conventional MPRAGE and DISORDER data, except for the amygdala and nucleus accumbens (motion-free, 0.38-0.65; motion- corrupt, 0.1-0.42). However, these values were less consistent for motion-corrupt conventional MPRAGE data for hippocampal volumes (motion-free 0.65-0.99; motion-corrupt, 0.11-0.91) and cortical measures (motion-free 0.76-0.98; motion- corrupt, 0.09-0.74). Mann-Whitney U showed percentage differences in measures obtained with motion-corrupt conventional MPRAGE compared to DISORDER data were significantly greater than in those obtained using motion-free conventional MPRAGE data in 22/58 structures. ConclusionIn the absence of motion, morphometric measures obtained using DISORDER are largely consistent with those from conventional MPRAGE data, whereas improved reliability is obtained by DISORDER for motion-degraded scans. This study validates DISORDER for brain morphometric studies in children.

neuroscience↗

bioRxiv2024

Spherical Echo-Planar Time-resolved Imaging (sEPTI) for rapid 3D quantitative T2* and Susceptibility imaging

PurposeTo develop a 3D spherical EPTI (sEPTI) acquisition and a comprehensive reconstruction pipeline for rapid high-quality whole-brain submillimeter T2* and QSM quantification. MethodsFor the sEPTI acquisition, spherical k-space coverage is utilized with variable echo-spacing and maximum kx ramp-sampling to improve efficiency and incoherency when compared to existing EPTI approaches. For reconstruction, an iterative rank-shrinking B0 estimation and odd-even high-order phase correction algorithms were incorporated into the reconstruction to better mitigate artifacts from field imperfections. A physics-informed unrolled network was utilized to boost the SNR, where 1-mm and 0.75-mm isotropic whole-brain imaging were performed in 45 and 90 seconds, respectively. These protocols were validated through simulations, phantom, and in vivo experiments. Ten healthy subjects were recruited to provide sufficient data for the unrolled network. The entire pipeline was validated on additional 5 healthy subjects where different EPTI sampling approaches were compared. Two additional pediatric patients with epilepsy were recruited to demonstrate the generalizability of the unrolled reconstruction. ResultssEPTI achieved 1.4 x faster imaging with improved image quality and quantitative map precision compared to existing EPTI approaches. The B0 update and the phase correction provide improved reconstruction performance with lower artifacts. The unrolled network boosted the SNR, achieving high-quality T2* and QSM quantification with single average data. High-quality reconstruction was also obtained in the pediatric patient using this network. ConclusionsEPTI achieved whole-brain distortion-free multi-echo imaging and T2* and QSM quantification at 0.75 mm in 90 seconds which has the potential to be useful for wide clinical applications.

bioengineering↗