Resolution and b value dependent structural connectome in ex vivo mouse brain

Crater, Stephanie; Maharjan, Surendra; Qi, Yi; Zhao, Qi; Cofer, Gary P.; Cook, James C.; Johnson, G. Allan; Wang, Nian

doi:10.1016/j.neuroimage.2022.119199

Cited by 15 publications

(17 citation statements)

References 111 publications

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“…Smaller voxels have fewer crossing fibers. Increased angular sampling aids in resolving these fibers 50 . We have previously demonstrated that the higher spatial/angular resolution reduces the false positives, 42 and these results are consistent with more recent studies 51 .…”

Section: Introductionsupporting

confidence: 89%

“…For example, the 36 μm 3 voxels used in this study have 1/(0.036) 3 (i.e., 21 000) times fewer fibers in any voxel, making distinction of the crossing fibers much easier. Accuracy in the connectome is also dependent on the angular resolution 45,50 . We have systematically studied the tradeoff in spatial and angular resolution in Reference 50 .…”

Section: Introductionmentioning

confidence: 99%

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Prenatal heroin exposure alters brain morphology and connectivity in adolescent mice

et al. 2022

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The United States is experiencing a dramatic increase in maternal opioid misuse and, consequently, the number of individuals exposed to opioids in utero. Prenatal opioid exposure has both acute and long-lasting effects on health and wellbeing. Effects on the brain, often identified at school age, manifest as cognitive impairment, attention deficit, and reduced scholastic achievement. The neurobiological basis for these effects is poorly understood. Here, we examine how in utero exposure to heroin affects brain development into early adolescence in a mouse model. Pregnant C57BL/6J mice received escalating doses of heroin twice daily on gestational days 4-18. The brains of offspring were assessed on postnatal day 28 using 9.4 T diffusion MRI of postmortem specimens at 36 μm resolution. Whole-brain volumes and the volumes of 166 bilateral regions were compared between heroin-exposed and control offspring. We identified a reduction in whole-brain volume in heroin-exposed offspring and heroin-associated volume changes in 29 regions after standardizing for whole-brain volume. Regions with bilaterally reduced standardized volumes in heroin-exposed offspring relative to controls include the ectorhinal and insular cortices. Regions with bilaterally increased standardized volumes in heroin-exposed offspring relative to controls include the periaqueductal gray, septal region, striatum, and hypothalamus. Leveraging microscopic resolution diffusion tensor imaging and precise regional parcellation, we generated whole-brain structural MRI diffusion connectomes. Using a dimension reduction approach with multivariate analysis of variance to assess group differences in the connectome, we found that in utero heroin exposure altered structure-based connectivity of the left septal region and the region that acts as a hub for limbic regulatory actions. Consistent with clinical evidence, our findings suggest that prenatal opioid exposure may have effects on brain morphology, connectivity, and, consequently, function that persist into adolescence.

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Section: Introductionsupporting

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Prenatal heroin exposure alters brain morphology and connectivity in adolescent mice

et al. 2022

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“…A high-sensitivity cryogenic RF surface receive-only coil was used for signal reception (Bruker CryoProbe). A multi-shot 3D EPI pulse sequence was used with the following parameters: matrix size = 180 × 128 × 76, FOV = 18.0 mm × 12.8 mm × 7.6 mm, 100 μm isotropic spatial resolution, TE = 22.3 ms, TR = 100 ms, 61 unique diffusion directions with b -value of 3000 s/mm 2 and six non-diffusion-weighted (b0) measurements ( Crater et al, 2022 ). The gradient separation time was 4.4 ms and the diffusion gradient duration time was 9.8 ms.…”

Section: Methodsmentioning

confidence: 99%

Age-dependent microstructure alterations in 5xFAD mice by high-resolution diffusion tensor imaging

Maharjan

Tsai²,

Lin³

et al. 2022

Front. Neurosci.

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PurposeTo evaluate the age-dependent microstructure changes in 5xFAD mice using high-resolution diffusion tensor imaging (DTI).MethodsThe 5xFAD mice at 4, 7.5, and 12 months and the wild-type controls at 4 months were scanned at 9.4T using a 3D echo-planar imaging (EPI) pulse sequence with the isotropic spatial resolution of 100 μm. The b-value was 3000 s/mm2 for all the diffusion MRI scans. The samples were also acquired with a gradient echo pulse sequence at 50 μm isotropic resolution. The microstructure changes were quantified with DTI metrics, including fractional anisotropy (FA) and mean diffusivity (MD). The conventional histology was performed to validate with MRI findings.ResultsThe FA values (p = 0.028) showed significant differences in the cortex between wild-type (WT) and 5xFAD mice at 4 months, while hippocampus, anterior commissure, corpus callosum, and fornix showed no significant differences for either FA and MD. FA values of 5xFAD mice gradually decreased in cortex (0.140 ± 0.007 at 4 months, 0.132 ± 0.008 at 7.5 months, 0.126 ± 0.013 at 12 months) and fornix (0.140 ± 0.007 at 4 months, 0.132 ± 0.008 at 7.5 months, 0.126 ± 0.013 at 12 months) with aging. Both FA (p = 0.029) and MD (p = 0.037) demonstrated significant differences in corpus callosum between 4 and 12 months age old. FA and MD were not significantly different in the hippocampus or anterior commissure. The age-dependent microstructure alterations were better captured by FA when compared to MD.ConclusionFA showed higher sensitivity to monitor amyloid deposition in 5xFAD mice. DTI may be utilized as a sensitive biomarker to monitor beta-amyloid progression for preclinical studies.

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Section: Resultsmentioning

confidence: 99%

“…Acquiring high resolution MR data might be one of the solutions as it will reduce partial volume effect, so that smaller axon bundles can be more easily separated from surrounding tissues, but at an expense of longer data acquisition time (Anderson et al, 2020; Crater et al, 2022). Over the past decade, the compressed sensing (CS) technique has been widely used to speed up the MR data acquisition by under-sampling the q -space or the k - space (Aranda et al, 2015; Daducci et al, 2015; Menzel et al, 2011; Tobisch et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Towards reliable reconstruction of the mouse brain thalamocortical connectivity using diffusion MRI

Arefin

Lee

Liang

et al. 2022

Preprint

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Diffusion magnetic resonance imaging (dMRI) tractography has yielded intriguing insights into brain circuits and their relationship to behavior in response to gene mutations or neurological diseases across a number of species. Still, existing tractography approaches suffer from limited sensitivity and specificity, leading to uncertain interpretation of the reconstructed connections. Hence, in this study, we aimed to optimize the imaging and computational pipeline for reliable reconstruction of the mouse brain thalamocortical network. We developed a dMRI-based atlas of the mouse forebrain with structural labels imported from the Allen Mouse Brain Atlas (AMBA). Using the atlas and tracer data from the Allen Mouse Brain Connectivity Atlas (AMBCA) as ground truth, we investigated the accuracy of reconstructed node-to-node thalamocortical structural connectivity and effects of imaging and tractography parameters. Our results suggest that these parameters significantly affect tractography outcomes and our atlas can be used to investigate macroscopic structural connectivity in the mouse brain. Furthermore, tractography in mouse brain gray matter still face challenges and need improved imaging and tractography methods.

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Resolution and b value dependent structural connectome in ex vivo mouse brain

Cited by 15 publications

References 111 publications

Prenatal heroin exposure alters brain morphology and connectivity in adolescent mice

Prenatal heroin exposure alters brain morphology and connectivity in adolescent mice

Age-dependent microstructure alterations in 5xFAD mice by high-resolution diffusion tensor imaging

Towards reliable reconstruction of the mouse brain thalamocortical connectivity using diffusion MRI

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