A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology

Juan Eugenio Iglesias,Ricardo Insausti,Garikoitz Lerma-Usabiaga,Martina Bocchetta,Koen Van Leemput,Douglas N Greve,Andre Van Der Kouwe,Bruce Fischl,César Caballero-Gaudes,Pedro M Paz-Alonso

doi:10.1016/j.neuroimage.2018.08.012

Abstract

The human thalamus is a brain structure that comprises numerous, highly specific nuclei. Since these nuclei are known to have different functions and to be connected to different areas of the cerebral cortex, it is of great interest for the neuroimaging community to study their volume, shape and connectivity in vivo with MRI. In this study, we present a probabilistic atlas of the thalamic nuclei built using ex vivo brain MRI scans and histological data, as well as the application of the atlas to in vivo MRI segmentation. The atlas was built using manual delineation of 26 thalamic nuclei on the serial histology of 12 whole thalami from six autopsy samples, combined with manual segmentations of the whole thalamus and surrounding structures (caudate, putamen, hippocampus, etc.) made on in vivo brain MR data from 39 subjects. The 3D structure of the histological data and corresponding manual segmentations was recovered using the ex vivo MRI as reference frame, and stacks of blockface photographs acquired during the sectioning as intermediate target. The atlas, which was encoded as an adaptive tetrahedral mesh, shows a good agreement with previous histological studies of the thalamus in terms of volumes of representative nuclei. When applied to segmentation of in vivo scans using Bayesian inference, the atlas shows excellent test-retest reliability, robustness to changes in input MRI contrast, and ability to detect differential thalamic effects in subjects with Alzheimer's disease. The probabilistic atlas and companion segmentation tool are publicly available as part of the neuroimaging package FreeSurfer.

Highlights

The thalamus is a diencephalic structure located between the cortex and the midbrain
We present a probabilistic atlas of the thalamic nuclei built using ex vivo brain MRI scans and histological data, as well as the application of the atlas to in vivo MRI segmentation
We present a probabilistic atlas of the human thalamus and its nuclei, as well as surrounding anatomy

Summary

Introduction

The thalamus is a diencephalic structure located between the cortex and the midbrain. The thalamus is involved in the regulation of consciousness, sleep and alert states; the motor system; and spoken language (Sherman and Guillery, 2001). Fischl et al (2002) used a voxel-wise probabilistic atlas of anatomy and MRI intensities to segment the thalamus, along with a number of other brain structures; this method is implemented in the widespread, open-source package FreeSurfer (Fischl, 2012). A number of standard segmentation algorithms have been applied to thalamus segmentation in structural MRI, such as multi-atlas segmentation (Heckemann et al, 2006), fuzzy clustering (Amini et al, 2004), voxel classification (Zikic et al, 2013) or Bayesian segmentation (Puonti et al, 2016)

Methods

Discussion

Conclusion