Thalamic pathology has been linked to long-term accumulation of disability and cognitive impairment in MS. However, assessment of thalamic volume is highly challenging for automatic as well as manual segmentation techniques. The use of multiple image contrasts may improve segmentation quality. We investigated correlations of thalamic volume and cognitive performance in MS. We evaluated automatic segmentation and our new semi-manual segmentation using T1 and proton-density MRI. Results based on FreeSurfer segmentation failed to yield correlations of thalamic volume with cognitive performance in MS patients. Using semi-manual segmentation, significant correlations were found between cognitive impairment and regional thalamic atrophy in MS.