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There exists a need for more accurate functional localization through the registration of functional to anatomical magnetic resonance brain images. This paper introduces a new software tool, named NPTK, that has been developed at the Signal and Image Processing Laboratory of the University of Texas at Dallas for improved functional localization in single- subject analysis. This software toolkit is developed based on recently introduced non-rigid registration and field map distortion correction techniques, which has been validated via in-vivo validation of retrospective distortion correction in Echo- Planar Imaging. The paper provides an overview of the entire functional localization pipeline, an algorithmic description of the developed software, and a discussion on the performance and applications of the software.