title: A Hitchhiker's Guide to Functional Magnetic Resonance Imaging.
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.
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Medicine, University of MinhoBraga, Portugal; ICVS/3B's - PT Government Associate LaboratoryBraga, Portugal.
authors.forename: José M
authors.initials: JM
authors.lastname: Soares
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Medicine, University of MinhoBraga, Portugal; ICVS/3B's - PT Government Associate LaboratoryBraga, Portugal.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Magalhães
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Medicine, University of MinhoBraga, Portugal; ICVS/3B's - PT Government Associate LaboratoryBraga, Portugal.
authors.forename: Pedro S
authors.initials: PS
authors.lastname: Moreira
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Medicine, University of MinhoBraga, Portugal; ICVS/3B's - PT Government Associate LaboratoryBraga, Portugal; Department of Informatics, University of MinhoBraga, Portugal.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Sousa
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Medicine, University of MinhoBraga, Portugal; ICVS/3B's - PT Government Associate LaboratoryBraga, Portugal.
authors.forename: Edward
authors.initials: E
authors.lastname: Ganz
authors.affiliation: Neuropsychophysiology Lab, CIPsi, School of Psychology, University of Minho Braga, Portugal.
authors.forename: Adriana
authors.initials: A
authors.lastname: Sampaio
authors.affiliation: Department of Informatics, University of Minho Braga, Portugal.
authors.forename: Victor
authors.initials: V
authors.lastname: Alves
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Medicine, University of MinhoBraga, Portugal; ICVS/3B's - PT Government Associate LaboratoryBraga, Portugal.
authors.forename: Paulo
authors.initials: P
authors.lastname: Marques
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Medicine, University of MinhoBraga, Portugal; ICVS/3B's - PT Government Associate LaboratoryBraga, Portugal; Clinical Academic Center - BragaBraga, Portugal.
authors.forename: Nuno
authors.initials: N
authors.lastname: Sousa
keywords: acquisition; analysis; fMRI; hitchhiker's guide; preprocessing