This paper describes a project involving the optimization of the analysis process of FreeSurfer and ANTS Registration for neuroscience analytics of patients at risk of cognitive decline using Nipype. The paper details the process of discovering more about Nipype, learning to use a supercomputer, and implementing the open-source python code to fit the needs of the research lab. Nipype is a python-based initiative to unify the various software packages used within the neuroscience community for data analysis. This paper also serves as documentation of the steps taken to complete the project so that future students are able to continue the optimization process to result in one cohesive workflow in which data is able to flow through a unified pipeline of analysis in the future.