MRI/DWI mini atlas of the Thalamus, in vivo Human Brain Atlas.
Poster No:
2213
Submission Type:
Abstract Submission
Authors:
Mark Schira1, Mustafa Kassem2, Markus Barth3, Thomas Shaw4, Zoey Isherwood5, Brooklyn Wright5, George Paxinos2
Institutions:
1University of Wollongong, Wollongong, New South Wales, 2Neuroscience Research Australia, Randwick, NSW, 3Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia, 4Centre for Advanced Imaging, The University of Queensland, Brisbane, Queensland, 5University of Wollongong, Wollongong, NSW
First Author:
Co-Author(s):
Introduction:
Long considered as too challenging for most MRI, the thalamus has received increasing interests in recent years. However, in particular the segmentation of the thalamus based on in vivo MRI data is still challenging. The Human Brain Atlas project aims to provide an MRI atlas of the living human brain [1] (Schira et al. 2023), but with the detail presently only provided from histology based atlases of about 1000 structures [2] (Mai, Majtanik and Paxinos, 2015). Here we present a mini atlas of the thalamus, providing a guide to scientist investigating this crucial area 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 from the bed nucleus of the stria terminalis and the anterior commissure to the most anterior point at the pulvinar and the posterior commissure. The maps cover the entire thalamus and all in-between, detailing the mediodorsal and posterior thalamic nuclei to the centromedian and ventroanterior nuclei.
·Fig. 1 shows a coronal section of our atlas through the anterior commisure (x=0 mm).
·Fig. 2 showes a zoomed in coronal section 11.5 mm posterior to the anterior commissure (x = -11.5mm). The left panels shows a T1w image, while the right shows fibre orientation.
Conclusions:
Our extensive scanning and image processing scripts resulted in exceptional image quality, the basis for the HBA 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 and serves as 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.
Neuroanatomy, Physiology, Metabolism and Neurotransmission:
Subcortical Structures 2
White Matter Anatomy, Fiber Pathways and Connectivity
Neuroinformatics and Data Sharing:
Brain Atlases 1
Novel Imaging Acquisition Methods:
Anatomical MRI
Diffusion MRI
Keywords:
Atlasing
MRI
Open Data
STRUCTURAL MRI
Sub-Cortical
Thalamus
White Matter
WHITE MATTER IMAGING - DTI, HARDI, DSI, ETC
1|2Indicates the priority used for review
Provide references using author date format
[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.