Functional Magnetic Resonance Imaging (FMRI) is currently acquired in Time Series to detect non-invasively, in-vivo functional activity of the human brain, thus determining four dimentional data sets. Although detectable, due to the short time in betweeen the acquisition of the brain volumes, head motion is usually minimal, however its correction is quite relevant to the consistency of the analysis of the FMRI data. This book presents methodology and technology for registering FMRI Time Series. Math formulations are given along with software engineering descriptions of the algorithms employed for the specific task of FMRI alignment. The book also presents the code that implements the methodology, which was written combining ANSI C, Open GL and Matlab. The intended audience of this work is composed by undergraduate and graduate students in academic disciplines within the domain of computer science applications, applied signal processing and computational engineering. Nevertheless this book is intented for anyone in the interests of how computer science, mathematics and engineering may combine together to forge the developmental effort in the quest for the solution of a technical challenge.