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

Abstract

The human thalamus is a brain structure that comprises numerous, highly specific nuclei. Since these nuclei areknown to have different functions and to be connected to different areas of the cerebral cortex, it is of greatinterest for the neuroimaging community to study their volume, shape and connectivity in vivo with MRI. In thisstudy, we present a probabilistic atlas of the thalamic nuclei built using ex vivo brain MRI scans and histologicaldata, as well as the application of the atlas to in vivo MRI segmentation. The atlas was built using manualdelineation of 26 thalamic nuclei on the serial histology of 12 whole thalami from six autopsy samples, combinedwith 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 correspondingmanual segmentations was recovered using the ex vivo MRI as reference frame, and stacks of blockface photographsacquired during the sectioning as intermediate target. The atlas, which was encoded as an adaptivetetrahedral mesh, shows a good agreement with previous histological studies of the thalamus in terms of volumesof representative nuclei. When applied to segmentation of in vivo scans using Bayesian inference, the atlas showsexcellent test-retest reliability, robustness to changes in input MRI contrast, and ability to detect differentialthalamic effects in subjects with Alzheimer's disease. The probabilistic atlas and companion segmentation tool arepublicly available as part of the neuroimaging package FreeSurfer