title: Anatomical guidance for functional near-infrared spectroscopy: AtlasViewer tutorial.
abstract: Functional near-infrared spectroscopy (fNIRS) is an optical imaging method that is used to noninvasively measure cerebral hemoglobin concentration changes induced by brain activation. Using structural guidance in fNIRS research enhances interpretation of results and facilitates making comparisons between studies. AtlasViewer is an open-source software package we have developed that incorporates multiple spatial registration tools to enable structural guidance in the interpretation of fNIRS studies. We introduce the reader to the layout of the AtlasViewer graphical user interface, the folder structure, and user files required in the creation of fNIRS probes containing sources and detectors registered to desired locations on the head, evaluating probe fabrication error and intersubject probe placement variability, and different procedures for estimating measurement sensitivity to different brain regions as well as image reconstruction performance. Further, we detail how AtlasViewer provides a generic head atlas for guiding interpretation of fNIRS results, but also permits users to provide subject-specific head anatomies to interpret their results. We anticipate that AtlasViewer will be a valuable tool in improving the anatomical interpretation of fNIRS studies.
authors.affiliation: Center for Pain and the Brain , Harvard Medical School, 1 Autumn Street, Boston, Massachusetts 02215, United States ; Department of Anesthesiology , Perioperative, and Pain Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, United States.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Aasted
authors.affiliation: Department of Radiology , Athinoula Martinos Center for Biomedical Imaging, 149 13th Street, Charlestown, Massachusetts 02129, United States.
authors.forename: Meryem A
authors.initials: MA
authors.lastname: Yücel
authors.affiliation: University College London , Department of Medical Physics and Biomedical Engineering, Gower Street, London WC1E 6BT, United Kingdom.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Cooper
authors.affiliation: Department of Radiology , Athinoula Martinos Center for Biomedical Imaging, 149 13th Street, Charlestown, Massachusetts 02129, United States.
authors.forename: Jay
authors.initials: J
authors.lastname: Dubb
authors.affiliation: Chuo University , Faculty of Science and Engineering, 1-13-27 Kasuga, Bunkyo, Tokyo 112-8551, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Tsuzuki
authors.affiliation: Center for Pain and the Brain , Harvard Medical School, 1 Autumn Street, Boston, Massachusetts 02215, United States ; Department of Anesthesiology , Perioperative, and Pain Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, United States ; Department of Radiology , Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, United States ; Department of Psychiatry , McLean Hospital, 115 Mill Street, Belmont, Massachusetts 02478, United States.
authors.forename: Lino
authors.initials: L
authors.lastname: Becerra
authors.affiliation: Department of Anesthesiology , Perioperative, and Pain Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, United States.
authors.forename: Mike P
authors.initials: MP
authors.lastname: Petkov
authors.affiliation: Center for Pain and the Brain , Harvard Medical School, 1 Autumn Street, Boston, Massachusetts 02215, United States ; Department of Anesthesiology , Perioperative, and Pain Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, United States ; Department of Radiology , Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, United States ; Department of Psychiatry , McLean Hospital, 115 Mill Street, Belmont, Massachusetts 02478, United States.
authors.forename: David
authors.initials: D
authors.lastname: Borsook
authors.affiliation: Chuo University , Faculty of Science and Engineering, 1-13-27 Kasuga, Bunkyo, Tokyo 112-8551, Japan.
authors.forename: Ippeita
authors.initials: I
authors.lastname: Dan
authors.affiliation: Department of Radiology , Athinoula Martinos Center for Biomedical Imaging, 149 13th Street, Charlestown, Massachusetts 02129, United States.
authors.forename: David A
authors.initials: DA
authors.lastname: Boas
keywords: atlas; image reconstruction; near-infrared spectroscopy; photon migration; probe design; tutorial