  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
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.
