In neuroscience research, fMRI image analysis is a major approach to identify the relationships between brain region and behavior. fMRI provides delayed real time brain activity signals non-invasively. Spatial preprocessing and statistical analysis needs to be performed to find the brain region that is responsive to certain tasks or stimulations. This project introduce an implementation of a tailored fMRI image processing pipeline, FIONA (Functional Imaging Overlay for NAvigated TMS), based on Insight Toolkit (ITK). The major functionalities of the software include preprocessing (realignment, co- registration, spatial smoothing), GLM analysis, hypothesis testing and multiple comparison correction (mainly FDR). FIONA is designed for usual clinical users or fMRI analyst who may not be an expert in neuroscience. It is designed for navigated TMS as its intended use. We also did benchmarking on different ITK optimizers comparing their performance in realignment section, to select an overall best optimizer. We test our whole implementation on different level noisy fMRI datasets.