AUTHOR=Soares José M. , Magalhães Ricardo , Moreira Pedro S. , Sousa Alexandre , Ganz Edward , Sampaio Adriana , Alves Victor , Marques Paulo , Sousa Nuno TITLE=A Hitchhiker's Guide to Functional Magnetic Resonance Imaging JOURNAL=Frontiers in Neuroscience VOLUME=10 YEAR=2016 URL=https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2016.00515 DOI=10.3389/fnins.2016.00515 ISSN=1662-453X ABSTRACT=

Functional Magnetic Resonance Imaging (fMRI) studies have become increasingly popular both with clinicians and researchers as they are capable of providing unique insights into brain functions. However, multiple technical considerations (ranging from specifics of paradigm design to imaging artifacts, complex protocol definition, and multitude of processing and methods of analysis, as well as intrinsic methodological limitations) must be considered and addressed in order to optimize fMRI analysis and to arrive at the most accurate and grounded interpretation of the data. In practice, the researcher/clinician must choose, from many available options, the most suitable software tool for each stage of the fMRI analysis pipeline. Herein we provide a straightforward guide designed to address, for each of the major stages, the techniques, and tools involved in the process. We have developed this guide both to help those new to the technique to overcome the most critical difficulties in its use, as well as to serve as a resource for the neuroimaging community.