A Hitchhiker's guide to functional magnetic resonance imaging

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.This article has been developed under the scope of the project NORTE-01-0145-FEDER-000013, supported by the Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER). We are also thankful to FCT-ANR/NEU-OSD/0258/2012 founded by FCT/MEC. RM and PSM are supported by FCT fellowship grants, from the Ph.D.-iHES program, with the references PDE/BDE/113604/2015 and PDE/BDE/113601/2015, respectively. PM is supported by a grant from the project “Better mental health during ageing based on temporal prediction of individual brain ageing trajectories (TEMPO)” (Contract grant number: P-139977) funded by Fundação Calouste Gulbenkian.