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The human thalamus is a brain structure that comprises numerous, highlyspecific nuclei. Since these nuclei are known to have different functions andto be connected to different areas of the cerebral cortex, it is of greatinterest for the neuroimaging community to study their volume, shape andconnectivity in vivo with MRI. In this study, we present a probabilistic atlasof 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. Theatlas was built using manual delineation of 26 thalamic nuclei on the serialhistology of 12 whole thalami from six autopsy samples, combined with manualsegmentations of the whole thalamus and surrounding structures (caudate,putamen, hippocampus, etc.) made on in vivo brain MR data from 39 subjects. The3D structure of the histological data and corresponding manual segmentationswas recovered using the ex vivo MRI as reference frame, and stacks of blockfacephotographs acquired during the sectioning as intermediate target. The atlas,which was encoded as an adaptive tetrahedral mesh, shows a good agreement withwith previous histological studies of the thalamus in terms of volumes ofrepresentative nuclei. When applied to segmentation of in vivo scans usingBayesian inference, the atlas shows excellent test-retest reliability,robustness to changes in input MRI contrast, and ability to detect differentialthalamic effects in subjects with Alzheimer's disease. The probabilistic atlasand companion segmentation tool are publicly available as part of theneuroimaging package FreeSurfer.

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