Thalamic nuclei have been implicated in several neurological diseases. Thalamic nuclei parcellation from structural MRI is challenging due to poor intra-thalamic nuclear contrast while methods based on diffusion and functional MRI are affected by limited spatial resolution and image distortion. Existing multi-atlas based techniques are often computationally intensive and time-consuming. In this work, we propose a 3D convolutional neural network (CNN) based framework for thalamic nuclei parcellation using T1-weighted Magnetization Prepared Rapid Gradient Echo (MPRAGE) images. Transformation of images to an efficient representation has been proposed to improve the performance of subsequent classification tasks especially when working with limited labeled data. We investigate this by transforming the MPRAGE images to White-Matter-nulled MPRAGE (WMn-MPRAGE) contrast, previously shown to exhibit good intra-thalamic nuclear contrast, prior to the segmentation step. We trained two 3D segmentation frameworks using MPRAGE images (n = 35 subjects): (a) a native contrast segmentation (NCS) on MPRAGE images and (b) a synthesized contrast segmentation (SCS) where synthesized WMn-MPRAGE representation generated by a contrast synthesis CNN were used. Thalamic nuclei labels were generated using THOMAS, a multi-atlas segmentation technique proposed for WMn-MPRAGE images. The segmentation accuracy and clinical utility were evaluated on a healthy cohort (n = 12) and a cohort (n = 45) comprising of healthy subjects and patients with alcohol use disorder (AUD), respectively. Both the segmentation CNNs yielded comparable performances on most thalamic nuclei with Dice scores greater than 0.84 for larger nuclei and at least 0.7 for smaller nuclei. However, for some nuclei, the SCS CNN yielded significant improvements in Dice scores (medial geniculate nucleus, P = 0.003, centromedian nucleus, P = 0.01) and percent volume difference (ventral anterior, P = 0.001, ventral posterior lateral, P = 0.01) over NCS. In the AUD cohort, the SCS CNN demonstrated a significant atrophy in ventral lateral posterior nucleus in AUD patients compared to healthy age-matched controls (P = 0.01), agreeing with previous studies on thalamic atrophy in alcoholism, whereas the NCS CNN showed spurious atrophy of the ventral posterior lateral nucleus. CNN-based segmentation of thalamic nuclei provides a fast and automated technique for thalamic nuclei prediction in MPRAGE images. The transformation of images to an efficient representation, such as WMn-MPRAGE, can provide further improvements in segmentation performance.