Purpose: Deep brain stimulation (DBS) relies on precise targeting of key structures such as the subthalamic nucleus (STN)for Parkinson’s disease (PD) and the ventro-intermedius nucleus of the thalamus (Vim) for essential tremor (ET). Segmentation software, such as GuideXT© and Suretune©, are commercially available for atlas-based identification of deep brain structures. However, no study has compared the concordance of the segmentation results between the two software. Methods: We retrospectively compared the concordance of segmentation of GuideXT© and Suretune© software by comparing the position of the segmented key structures with clinically predicted targets obtained using the newly developed RebrAIn© software as a reference. Results: We targeted the STN in 44 MRI from PD patients (88 hemispheres) and the Vim in 31 MRI from ET patients (62 hemispheres) who were elected for DBS. In 22 STN targeting (25%), the target positioning was not correlating between GuideXT© and Suretune©. Regarding the Vim, targets were located in the segmented Vim in 37%, the posterior subthalamic area (PSA) in 60%, and the STN in 3% of the cases using GuideXT©; the proportions were 34%, 60%, and 6%, respectively, using Suretune©. The mean distance from the centre of the RebrAIn© targeting to the segmented Vim by Suretune© was closer (0.64 mm) than with GuideXT© (0.96 mm; p = 0.0004). Conclusion: While there is some level of concordance in the segmentation results of key structures for DBS treatment among software models, differences persist. Therefore, such software should still be considered as tools and should not replace clinician experience in DBS planning.