Preoperative fMRI is one of the best established clinical fMRI applications. Due to the difficulties in recording and coregistration of functional image data, we present methods to standardize and automate these procedures. We used a self-made interactive software package (AFI - Automated Functional Imaging) to automate the time consuming and complex analysis of fMRI data. AFI controls the BrainVoyager program, a postprocessing software package, and furthermore facilitates data management, anonymization of patient data, storage, documentation, data export to neuronavigation systems and the opportunity of spatial transformation of image data for use in group studies. By the end of 2006 we have used this method on 123 patients with brain tumors and 47 patients with trigeminal neuralgia. The fundamental basis of multimodal neuronavigation is precise coregistration. EPI images contain spatial distortions of 5-15 mm. We were able to reduce the misregistration of EPI and FLASH images in a selectable region of interest to 1-2 mm. Furthermore AFI reduces the average evaluation time for a standard clinical fMRI study (four functional measurements, one anatomical data set) by approx. 50% from 140 minutes to about 70 minutes in comparison to manual evaluation by an expert. More importantly, the personal attendance time required for the evaluation decreases by 84% to 23 minutes as the remainder of the program runs automatically. In comparison to currently available online postprocessing software tools which are more limited in use, BrainVoyager can be used for coregistration, data export to neuronavigation systems and spatial transformation.