Surface-based parcellation and vertex-wise analysis of ultra high-resolution ex vivo 7 tesla MRI in neurodegenerative diseases

Magnetic resonance imaging (MRI) is the standard modality to understand human brain structure and function in vivo (antemortem). Decades of research in human neuroimaging has led to the widespread development of methods and tools to provide automated volume-based segmentations and surface-based parcellations which help localize brain functions to specialized anatomical regions. Recently ex vivo (postmortem) imaging of the brain has opened-up avenues to study brain structure at sub-millimeter ultra high-resolution revealing details not possible to observe with in vivo MRI. Unfortunately, there has been limited methodological development in ex vivo MRI primarily due to lack of datasets and limited centers with such imaging resources. Therefore, in this work, we present one-of-its-kind dataset of 82 ex vivo T2w whole brain hemispheres MRI at 0.3 mm isotropic resolution spanning Alzheimer's disease and related dementias. We adapted and developed a fast and easy-to-use automated surface-based pipeline to parcellate, for the first time, ultra high-resolution ex vivo brain tissue at the native subject space resolution using the Desikan-Killiany-Tourville (DKT) brain atlas. This allows us to perform vertex-wise analysis in the template space and thereby link morphometry measures with pathology measurements derived from histology. We will open-source our dataset docker container, Jupyter notebooks for ready-to-use out-of-the-box set of tools and command line options to advance ex vivo MRI clinical brain imaging research on the project webpage.

Automated deep learning segmentation of high-resolution 7 T ex vivo MRI for quantitative analysis of structure-pathology correlations in neurodegenerative diseases

Ex vivo MRI of the brain provides remarkable advantages over in vivo MRI for visualizing and characterizing detailed neuroanatomy, and helps to link microscale histology studies with morphometric measurements. However, automated segmentation methods for brain mapping in ex vivo MRI are not well developed, primarily due to limited availability of labeled datasets, and heterogeneity in scanner hardware and acquisition protocols. In this work, we present a high resolution dataset of 37 ex vivo post-mortem human brain tissue specimens scanned on a 7T whole-body MRI scanner. We developed a deep learning pipeline to segment the cortical mantle by benchmarking the performance of nine deep neural architectures. We then segment the four subcortical structures: caudate, putamen, globus pallidus, and thalamus; white matter hyperintensities, and the normal appearing white matter. We show excellent generalizing capabilities across whole brain hemispheres in different specimens, and also on unseen images acquired at different magnetic field strengths and different imaging sequence. We then compute volumetric and localized cortical thickness measurements across key regions, and link them with semi-quantitative neuropathological ratings. Our code, containerized executables, and the processed datasets are publicly available at: https://github.com/Pulkit-Khandelwal/upenn-picsl-brain-ex-vivo.

Gray Matter Segmentation in Ultra High Resolution 7 Tesla ex vivo T2w MRI of Human Brain Hemispheres

Ex vivo MRI of the brain provides remarkable advantages over in vivo MRI for visualizing and characterizing detailed neuroanatomy. However, automated cortical segmentation methods in ex vivo MRI are not well developed, primarily due to limited availability of labeled datasets, and heterogeneity in scanner hardware and acquisition protocols. In this work, we present a high resolution 7 Tesla dataset of 32 ex vivo human brain specimens. We benchmark the cortical mantle segmentation performance of nine neural network architectures, trained and evaluated using manually-segmented 3D patches sampled from specific cortical regions, and show excellent generalizing capabilities across whole brain hemispheres in different specimens, and also on unseen images acquired at different magnetic field strength and imaging sequences. Finally, we provide cortical thickness measurements across key regions in 3D ex vivo human brain images. Our code and processed datasets are publicly available at https://github.com/Pulkit-Khandelwal/picsl-ex-vivo-segmentation.