MRI/DWI mini atlas of the Thalamus, Hippocampus, and Cerebellum, in vivo Human Brain Atlas
Poster No:
1801
Submission Type:
Abstract Submission
Authors:
Steve Kassem1, Brooklyn Wright2, Mark Schira3, George Paxinos4
Institutions:
1Neuroscience Research Australia, Sydney, New Sotuh Wales, 2University of New South Wales, Gledswood Hills, New South Wales, 3University of Wollongong, Wollongong, NSW, 4Neuroscience Research Australia, Sydney, NSW
First Author:
Co-Author(s):
Introduction:
Despite improvements in MRI power and processing, the thalamus, hippocampus and cerebellum still have difficulty in being mapped/segmented in MRI. With most delineations coming from, or being informed by, histology, because of these lower MRI resolutions, segmentation of these structures using in vivo MRI data is challenging. The Human Brain Atlas project aims to provide an ultra-high-resolution MRI atlas of the living human brain (Schira et al. 2023) with isotropic resolution rivalling the detail of histology, permitting the segmentation of about 1000 structures in vivo. (Mai, Majtanik and Paxinos, 2015). Here we present a mini atlas, from this broader project, of the thalamus, hippocampus, and cerebellum, providing a guide to scientists investigating these crucial areas of the human brain.
Methods:
Multiple acquisitions were collected for each contrast for each participant (20 T1w, 12 T2w, 10 DWI scans), and were averaged using symmetric group-wise normalisation (Advanced Normalisation Tools). T1w and T2w data were acquired using a 7T human research scanner (Siemens MAGNETOM) at the Centre for Advanced Imaging, University of Queensland. T1w scans were recorded using a MP2RAGE sequence (WIP944) at 0.4 mm isotropic resolution, T2w scans were recorded using TSE sequence (WIP692) at 0.4 mm isotropic resolution with the parameters: DWI scans were recorded with a human 3T MRI (Philips Achieva CX) (NeuRA Imaging Centre) using an inverse blip corrected SPIR sequence at 1.25 mm isotropic resolution. Using ANTsMultivariateTemplate fitting these datasets were combined into a combined space at 0.25mm.
Results:
The resulting image quality permits structural parcellations rivalling histology-based atlases, while maintaining the advantages of in vivo MRI. Our data are virtually distortion free, fully 3D, and compatible with existing in vivo Neuroimaging analysis tools. Our data is available for open access under https://osf.io/ckh5t/. Using manual, digitized pen and paper tracings we delineated the entire thalamus, hippocampus, and cerebellum; from the anterior commissure to the posterior commissure and the cerebellum. The maps cover the entire thalamus, hippocampus and cerebellum, with the aim to continually add more regions to this atlas until comprehensive.
Conclusions:
Our extensive scanning and image processing scripts resulted in exceptional image quality, the basis for the Human Brain Atlas project. In particular for the DWI data, combining effectively over 400 images resulted in remarkably improved detail and resolution. Our detailed segmentation resulted in the most comprehensive and detailed MRI map of the human in vivo thalamus, hippocampus and cerebellum, and serves as a template. We argue that the dataset presented herein and made available for open access [1] satisfies the new needs for a modern 3D atlas of the human brain. Importantly it uses contrast that is immediately familiar to the user of MRI. It can inform researchers, clinicians and educators
Modeling and Analysis Methods:
Diffusion MRI Modeling and Analysis
Methods Development
Neuroinformatics and Data Sharing:
Brain Atlases 1
Novel Imaging Acquisition Methods:
Anatomical MRI 2
Diffusion MRI
Keywords:
HIGH FIELD MR
MRI
NORMAL HUMAN
STRUCTURAL MRI
Other - Atlas
1|2Indicates the priority used for review
Abstract Information
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[2] Mai, J.K., Majtanik, M. and Paxinos, G., 2015. Atlas of the human brain. Academic Press.
Garey, L.J. ed., 1999. Brodmann's' localisation in the cerebral cortex'. World Scientific.
von Economo, C.F. and Koskinas, G.N., 1925. Die cytoarchitektonik der hirnrinde des erwachsenen menschen. J. Springer.