The Gegenbauer image reconstruction method, previously shown to improve the quality of magnetic resonance images, is utilized in this study as a segmentation preprocessing step. It is demonstrated that, for all simulated and real magnetic resonance images used in this study, the Gegenbauer reconstruction method improves the accuracy of segmentation. Although it is more desirable to use the k-space data for the Gegenbauer reconstruction method, only information acquired from MR images is necessary for the reconstruction, making the procedure completely self-contained and viable for all human brain segmentation algorithms.