Biology subjects

Seifert, A. C.

Publications and source records attributed to Seifert, A. C..

5 recordsLinked to original sources

bioRxiv2025

Multi-center benchmarking of cervical spinal cord RF coils for 7 T MRI: A traveling spines study

PurposeThe depth within the body, small diameter, long length, and varying tissue surrounding the spinal cord impose specific considerations when designing radiofrequency coils. The optimal coil configuration for 7 T cervical spinal cord MRI is unknown and, currently, there are very few coil options. The purpose of this work was (1) to establish a quality control protocol for evaluating 7 T cervical spinal cord coils and (2) to use that protocol to evaluate the performance of 4 different coil designs. MethodsThree healthy volunteers and a custom anthropomorphic phantom (the traveling spines cohort) were scanned at seven 7 T imaging centers using a common protocol and each centers specific cervical spinal cord coil. Four different coil designs were tested (two in-house, one Rapid Biomedical, and one MRI.TOOLS design). ResultsThe Rapid Biomedical coil was found to have the highest B1+ efficiency, whereas one of the in-house designs (NeuroPoly Lab) had the highest SNR and the largest spinal cord coverage. The MRI.TOOLS coil had the most uniform B1+ profile along the cervical spinal cord; however, it was limited in its ability to provide the requested flip angles (especially for larger individuals). The latter was also the case for the second in-house coil (MSSM). ConclusionThe results of this study serve as a guide for the spinal cord MRI community in selecting the most suitable coil based on specific requirements and offer a standardized protocol for assessing future coils.

bioengineering↗

bioRxiv2023

Thermal Stimulus Task fMRI in the Cervical Spinal Cord at 7 Tesla

PurposeAlthough functional MRI is widely applied in the brain, fMRI of the spinal cord is more technically demanding. Proximity to the vertebral column and lungs results in strong spatial inhomogeneity and temporal fluctuations in B0. Increasing field strength enables higher spatial resolution and improved sensitivity to BOLD signal, but amplifies the effects of B0 inhomogeneity. In this work, we present the first task fMRI in the spinal cord at 7 T. Further, we compare the performance of single-shot and multi-shot 2D EPI protocols, which differ in sensitivity to spatial and temporal B0 inhomogeneity. MethodsThe cervical spinal cords of 11 healthy volunteers were scanned at 7 T using single-shot 2D EPI at 0.75 mm in-plane resolution and multi-shot 2D EPI at 0.75 and 0.6 mm in-plane resolutions. All protocols used 3 mm slice thickness. For each protocol, the BOLD response to thirteen 10-second noxious thermal stimuli applied to the right thumb was acquired in a 10-minute fMRI run. Image quality, temporal SNR, and BOLD activation (percent signal change and z-stat) at both individual-and group-level were evaluated between the protocols. ResultsTemporal SNR was highest in single-shot and multi-shot 0.75 mm protocols. In group-level analyses, activation clusters appeared in all protocols in the ipsilateral dorsal quadrant at the expected C6 neurological level. In individual-level analyses, activation clusters at the expected level were detected in some, but not all subjects and protocols. Single-shot 0.75 mm generally produced the highest mean z-statistic, while multi-shot 0.60 mm produced the best-localized activation clusters and the least geometric distortion. Larger than expected within-subject segmental variation of BOLD activation along the cord was observed. ConclusionGroup-level sensory task fMRI of the cervical spinal cord is feasible at 7 T with single-shot or multi-shot EPI. The best choice of protocol will likely depend on the relative importance of sensitivity to activation versus spatial localization of activation for a given experiment. HighlightsFirst stimulus task fMRI results in the spinal cord at 7 T Single-shot 0.75 mm 2D EPI produced the highest mean z-statistic Multi-shot 0.60 mm 2D EPI provided the best-localized activation and least distortion

bioengineering↗

bioRxiv2022

A single closed head injury in mice induces chronic, progressive white matter atrophy and increased phospho-tau expressing oligodendrocytes

Traumatic brain injury (TBI) acutely damages the brain; this injury can evolve into chronic neurodegeneration. While much is known about the chronic effects arising from multiple mild TBIs, far less is known about the long-term effects of a single moderate to severe TBI. We found that a single moderate closed head injury to mice induces diffuse axonal injury within 1-day post-injury (DPI). At 14 DPI, injured animals have atrophy of ipsilesional cortex, thalamus, and corpus callosum, with bilateral atrophy of the dorsal fornix. Atrophy of the ipsilesional corpus callosum is accompanied by decreased fractional anisotropy and increased mean and radial diffusivity that remains unchanged between 14 and 180 DPI. Injured animals increased density of phospho-tau immunoreactive (pTau+) cells in the ipsilesional cortex and thalamus, and bilaterally in corpus callosum. Between 14 and 180 DPI, atrophy occurs in the ipsilesional ventral fornix, contralesional corpus callosum, and bilateral internal capsule. Diffusion tensor MRI parameters remain unchanged in white matter regions with delayed atrophy. Between 14 and 180 DPI, pTau+ cell density increases bilaterally in corpus callosum, but decreases in cortex and thalamus. The location of pTau+ cells within the ipsilesional corpus callosum changes between 14 and 180 DPI; density of all cells increases including pTau+ or pTau- cells. Greater than 90% of the pTau+ cells are in the oligodendrocyte lineage in both gray and white matter. Density of thioflavin-S+ cells in thalamus increases by 180 DPI. These data suggest a single closed head impact produces multiple forms of chronic neurodegeneration. Gray and white matter regions proximal to the impact site undergo rapid atrophy. More distal white matter regions undergo chronic, progressive white matter atrophy with an increasing density of oligodendrocytes containing pTau. These data suggest that the chronic neurodegeneration arising from a single moderate CHI differs greatly from the chronic traumatic encephalopathy produced by multiple mild head injuries. HighlightsGray and white matter atrophy begins within 14 days after a single closed head injury White matter atrophy progresses between 14 and 180 days post injury with minimal changes in diffusion tensor MRI parameters. CHI increases the density of oligodendrocytes with perinuclear accumulation of phosphorylated tau Thioflavin-S+ cells increase in thalamus at 180 days post injury

neuroscience↗

bioRxiv2022

Impact of Autocalibration Method on Accelerated Echo-Planar Imaging of the Cervical Spinal Cord at 7T

PurposeThe spinal cord contains sensorimotor neural circuits of scientific and clinical interest. However, spinal cord fMRI is significantly more technically demanding than brain fMRI due primarily to its proximity to the lungs. Accelerated EPI at 7T is particularly vulnerable to k-space phase inconsistencies induced by motion or B0 fluctuation, during either autocalibration signal (ACS) or timeseries acquisition. For 7T brain fMRI, sensitivity to motion and B0 fluctuation can be reduced using a re-ordered segmented EPI ACS based on the fast low-angle excitation echo-planar technique (FLEET). However, respiration-induced B0 fluctuations (exceeding 100Hz at C7) are greater, and fewer k-space lines per slice are required, for cervical spinal cord fMRI at 7T, necessitating a separate evaluation of ACS methods. MethodsWe compared 24-line single-shot EPI, and 48-line two-shot segmented EPI, two-shot FLEET, and GRE-based ACS acquisition methods, performed under various physiological conditions, in terms of temporal SNR (tSNR) and prevalence of artifacts in GRAPPA-accelerated EPI of the cervical spinal cord at 7T. ResultsSegmented EPI and FLEET ACS produce images with nearly identical patterns of severe image artifacts. GRE and single-shot EPI ACS consistently produce images free from significant artifacts, and tSNR is significantly greater for GRE ACS, particularly in lower slices where through-slice dephasing is most severe. ConclusionGRE and single-shot EPI ACS acquisition methods, which are robust to respiration-induced phase errors between k-space segments, produce images with fewer and less severe artifacts than either FLEET or conventionally segmented EPI for accelerated EPI of the cervical spinal cord at 7T.

bioengineering↗

bioRxiv2019

Formalin Tissue Fixation Biases Myelin-Sensitive MRI

PurposeChemical fixatives, such as formalin, form cross-links between proteins and affect the relaxation times and diffusion properties of tissue. These fixation-induced changes likely also affect myelin density measurements produced by quantitative magnetization transfer (qMT) and myelin water imaging (MWI). In this work, we evaluate these myelin-sensitive MRI methods for fixation-induced biases. MethodsWe perform qMT, MWI, and D2O-exchanged zero echo-time (ZTE) imaging on unfixed human spinal cord tissue, and repeat these measurements after 1 day and 31 days of formalin fixation. ResultsThe qMT bound pool fraction increased by 30.7{+/-}21.1% after 1 day of fixation and by 42.6{+/-}33.9% after 31 days of fixation. Myelin water fraction increased by 39.7{+/-}15.5% and 37.0{+/-}15.9% at these same time points, and mean T2 of the myelin water pool nearly doubled. Reference-normalized D2O-exchanged ZTE signal intensity increased by 8.17{+/-}6.03% after 31 days of fixation, but did not change significantly after 1 day of fixation. After fixation, specimen cross-sectional area decreased by approximately 5%; after correction for shrinkage, changes in D2O-exchanged ZTE intensity were nearly eliminated. ConclusionF and MWF are significantly increased by formalin fixation, while D2O-exchanged ZTE intensity is minimally affected. Changes in qMT and MWI may be due, in part, to delamination and formation of vacuoles in the myelin sheath. D2O-exchanged signal intensity may be altered by fixation-induced changes in myelin lipid solid-state 1H T1. We urge caution in the comparison of these measurements across subjects or specimens in different states, especially unfixed vs. fixed tissue.

neuroscience↗