Tensor Image Registration Library: Automated Deformable Registration of Stand-Alone Histology Images to Whole-Brain Post-Mortem MRI Data

Huszár, I; Pallebage-Gamarallage, Menuka; Bangerter-Christensen, Sarah; Brooks, Hannah; Fitzgibbon, Sean; Foxley, Sean; Hiemstra, Marlies; Howard, Amy; Jbabdi, Saâd; Kor, Daniel; Leonte, Anna; Mollink, Jeroen; Smart, Adele; Tendler, Benjamin C.; Turner, Martin R.; Ansorge, Olaf; Miller, Karla L.; Jenkinson, Mark

doi:10.1101/2022.08.11.503605

Cited by 2 publications

(2 citation statements)

References 59 publications

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“…6.2 MRI-Microscopy data co-registration MRI-Microscopy registration was performed using TIRL (v3.1.1), an automated pipeline facilitating the accurate registration of the histology sections to the whole brain MRI via a sequence of linear and non-linear transformations (see 29,36,75,76 for further details). Here each PLI, myelin-and Nissl-stained slide was registered independently to the MRI space.…”

Section: Mri Data and Microscopy Data Acquisitionmentioning

confidence: 99%

Imaging the structural connectome with hybrid diffusion MRI-microscopy tractography

Zhu,

Huszar,

Cottaar

et al. 2024

Preprint

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Neuroanatomical tract tracing methods are fundamental in providing “gold standard” estimates of brain connectivity. However, tracer methods cannot be performed in humans and even in animals, we can only study projections from typically one or two injection sites per animal sacrificed. Orientation-sensitive microscopy techniques such as PLI provide an alternative where they can visualise detailed fibre orientations at the micron-scale across the whole brain. However, these methods are often most informative on orientations within the 2D imaging plane, with less reliable or missing through-plane information, restricting 3D tract reconstruction. Conversely, dMRI can estimate fibre orientations in 3D but at low resolution, which leads to many false positive and negative estimates of fibre trajectories.To facilitate reconstruction of the microscopy-informed connectome, we develop a data-fusion method that complements 2D microscopy with through-plane information from diffusion MRI to construct 3D hybrid orientations that are both maximally informed by the high-resolution microscopy, have whole-brain coverage and can be input into existing tractography pipelines. Diffusion MRI can be readily acquired prior to microscopy meaning the same method is translatable across species, including in humans. Here we apply our method to an existing open-access macaque dataset and demonstrate (1) whole-brain microscopy-informed tractography (2) the advantages of hybrid tractography in two known tractography challenges, the gyral bias and bottleneck problem (3) how hybrid tractography appears to outperform diffusion-only tractography when compared to tracer data and (4) the generalisability of our hybrid method to different microscopy contrasts, facilitating wider translation.

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Section: Mri Data and Microscopy Data Acquisitionmentioning

confidence: 99%

Imaging the structural connectome with hybrid diffusion MRI-microscopy tractography

Zhu,

Huszar,

Cottaar

et al. 2024

Preprint

Self Cite

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“…We also accessed previously generated registrations for each histology slice to the MGE volume. These registrations were derived using FSL's TIRL 100,101 .…”

Section: Macaque -Histological Datamentioning

confidence: 99%

Hippocampal connectivity patterns echo macroscale cortical evolution in the primate brain

Eichert,

DeKraker,

Howard

et al. 2023

Preprint

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The hippocampus is involved in numerous cognitive functions, some of which have uniquely human aspects, such as autobiographical memory. Hippocampal anatomy, however, is typically considered conserved across primates and its evolutionary diversification is rarely studied. Comparing hippocampal structure and function is, therefore, critical for understanding human brain architecture. Here, we developed a novel comparative framework to study the hippocampus across species characterising its geometry, microstructure, and functional network embedding. In humans and macaques, we generated a new comparative space that represents the hippocampus as an unfolded surface, which respects its sheet-like anatomy. We mapped histological and MRI-derived markers of microstructure to the hippocampal surface and integrated it with low-dimensional embedding of resting-state MRI connectivity data. Our results demonstrate that the micro– and macro-structural organisation of the hippocampus are overall conserved in both species, showing consistent anterior-posterior and subfield-to-subfield differentiation. Furthermore, while hippocampal functional organisation also follows anterior-posterior trends in both species, hippocampal functional connectivity markedly reflected evolutionary reconfiguration of transmodal networks, in particular the default-mode network. Specifically, the inferior parietal lobe in the macaque mirrors an incomplete integration of the default mode network in non-human primates. By combining fine-grained anatomical investigation with large-scale functional imaging, we showed that microstructurally preserved regions like the hippocampus may still undergo functional reconfiguration, due to their embedding in higher-order association networks.SummaryWhile the hippocampus is key for uniquely human cognitive abilities, it is also a phylogenetically old cortex and paradoxically considered evolutionarily preserved. Here, we introduce a comparative framework to quantify preservation and reconfiguration of hippocampal organisation in primate evolution, by analysing the hippocampus as an unfolded cortical surface that is geometrically matched across species. Our findings revealed an overall conservation of hippocampal macro– and micro-structure, showing anterior-posterior and, perpendicularly, subfield-related organisational axes in both humans and macaques. However, while functional organisation in both species also followed an anterior-posterior axis, the latter showed a marked evolutionary reconfiguration, which mirrors a rudimentary integration of the default-mode-network in non-human primates. Our findings suggest that microstructurally preserved regions like the hippocampus may still undergo functional reconfiguration in primate evolution, due to their embedding in heteromodal association networks.

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Tensor Image Registration Library: Automated Deformable Registration of Stand-Alone Histology Images to Whole-Brain Post-Mortem MRI Data

Cited by 2 publications

References 59 publications

Imaging the structural connectome with hybrid diffusion MRI-microscopy tractography

Imaging the structural connectome with hybrid diffusion MRI-microscopy tractography

Hippocampal connectivity patterns echo macroscale cortical evolution in the primate brain

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