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Neuroimage. 2017 Sep;158:430-440. doi: 10.1016/j.neuroimage.2017.06.047. Epub 2017 Jun 29.

Thalamus segmentation using multi-modal feature classification: Validation and pilot study of an age-matched cohort.

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Department of Electrical and Computer Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA. Electronic address:
Department of Electrical and Computer Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA; Department of Computer Science, The Johns Hopkins University, Baltimore, MD 21218, USA.
Department of Interdisciplinary Studies, University of Maryland, Baltimore County, MD 21250, USA.
Department of Computer Science, Bucknell University, Lewisburg, PA 17837, USA.
Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.


Automatic segmentation of the thalamus can be used to measure differences and track changes in thalamic volume that may occur due to disease, injury or normal aging. An automatic thalamus segmentation algorithm incorporating features from diffusion tensor imaging (DTI) and thalamus priors constructed from multiple atlases is proposed. Multiple atlases with corresponding manual thalamus segmentations are registered to the target image and averaged to generate the thalamus prior. At each voxel in a region of interest around the thalamus, a multidimensional feature vector that includes the thalamus prior as well as a set of DTI features, including fractional anisotropy, mean diffusivity, and fiber orientation is formed. A random forest is trained to classify each voxel as belonging to the thalamus or background within the region of interest. Using a leave-one-out cross-validation on nine subjects, the proposed algorithm achieves a mean Dice score of 0.878 and 0.890 for the left and right thalami, respectively, which are higher Dice scores than the three state-of-art methods we compared to. We demonstrate the utility of the method with a pilot study exploring the difference in the thalamus fraction between 21 multiple sclerosis (MS) patients and 21 age-matched healthy controls. The left and right thalamic volumes (normalized by intracranial volumes) are larger in healthy controls by 7.6% and 7.3% respectively, compared to MS patients (though neither result is statistically significant).


Diffusion MRI; Magnetic resonance imaging; Thalamus segmentation

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