openfnirs

Welcome to the openfnirs.org website!

Our mission is to foster the development of an fNIRS ecosystem and to promote the open dissemination of fNIRS hardware and software, as well as provide access to resources, documentation and training opportunities for fNIRS users.

We are funded by the National Institute of Health NIH grant R24-NS104096 “Establishing an fNIRS Ecosystem for Open Software-Hardware Dissemination.”

What is fNIRS?

Functional Near-Infrared Spectroscopy (fNIRS) is a non-invasive, portable method employing near-infrared light propagating diffusely through the scalp and brain, for functional monitoring and imaging of human brain hemodynamics.

This neuroimaging modality is particularly suited for populations and studies where other imaging options are limited, such as infants, children, and volunteers/patients interacting freely with their environment. fNIRS has found a wide range of applications to study normal and pathological brain physiology, including perception and cognition, motor control, psychiatric conditions (depression, schizophrenia), and behavioral and cognitive development in infants and children.

More background information on NIRS can be found on the Scholarpedia webpage. More can be read in a 2017 special section in Neurophotonics that spanned 3 issues with 41 papers (part I, part II, part III). In addition, a 2014 special issue of NeuroImage provides a thorough review of the field, as well as publications on state-of-the-art applications. The introduction to the special issue can be found here. The Society for Functional Near Infrared Spectroscopy runs a conference every two years and hosts a Facebook page from which one can connect with the international fNIRS community.

Who are we?

The openfnirs.org website is developed by:

• The Boston University NeuroPhotonics Center under NIH grant R24-NS104096,
• Alexander von Lühmann who developed the opennirs.org website offering documentation and files for open NIRS instrumentation hardware,

Contact us

David Boas

 

 

 

BU NeuroPhotonics Center open hardware – ninjaNIRS

We are developing a wearable modular fNIRS system at the BU Neurophotonics Center that we call ninjaNIRS. We are sharing hardware designs and associated software for this system here.

Other open hardware

The site opennirs.org developed by Alexander von Lühmann provides documentation and technical details for  wearable, stand-alone, open NIRS instrumentation hardware.

Homer3

Homer3 is available at GitHub at here.  This is the latest installment in the HOMER software series for analyzing fNIRS data. It builds upon Homer2 by enabling custom processing scripts at the session and group levels. This will enable more powerful statistical analyses of session and group level results. Homer3 also implements the Shared NIR data Format (SNIRF) that has been developed and adopted by a broad consortium of software and hardware developers. Please join the Homer google group discussion forum here.

If you are publishing papers using Homer2 or Homer3, we request that you cite this paper:

Huppert, T., Diamond, S., Franceschini, M., Boas, D. (2009). HomER: a review of time-series analysis methods for near-infrared spectroscopy of the brain. Applied optics 48(10)https://dx.doi.org/10.1364/ao.48.00d280

If you are publishing papers using atlasViewer, we request that you cite this paper:

Aasted, C., Yücel, M., Cooper, R., Dubb, J., Tsuzuki, D., Becerra, L., Petkov, M., Borsook, D., Dan, I., Boas, D. (2015). Anatomical guidance for functional near-infrared spectroscopy: AtlasViewer tutorial Neurophotonics 2(2), 020801-020801. https://dx.doi.org/10.1117/1.NPh.2.2.020801

Homer2

After 10 years of developing the Homer2 and AtlasViewer toolboxes (2009 to 2019), Homer2 is now being replaced by Homer3. AtlasViewer will continue to evolve along with Homer3. Homer2 will remain available online. It is unlikely that any more revisions will be made to Homer2.

These sets of Matlab scripts are used for analyzing fNIRS data and enable estimation and mapping of brain activation.

Access to the open-source Homer2 and AtlasViewer software can be found at homer-fnirs.org.

Other fNIRS software

The resource page of the fnirs.org website provides a list of available software developed for use in fNIRS imaging. These include (let us know of others to add):

• fNIRSOFT, from Biopac Systems, Inc., USA
• fOSA-SPM, from the Biomedical Optics Research Laboratory (BORL) at University College London, UK
• Imperial College Near Infrared Spectroscopy Neuroimaging Analysis (ICNNA), from the Imperial College London, UK
• NAP (NIRS Analysis Package), from the Laboratory of Computational Neurodiagnostics at Stony Brook University, USA
• NIRFAST, from the the Optics in Medicine Laboratory at Dartmouth College, USA
• NIRS-SPM, from the Bio Imaging & Signal Processing Lab at KAIST, South Korea
• NIRx NIRSlab
• NIRS Toolbox, from the Huppert Lab at the University of Pittsburgh, USA
• NIRSTORM, from the PERFORM Center at Concordia University, Canada
• MCX/MMC, from Northeastern University, USA
• PHOEBE, from the University of Houston, USA
• POTATo
• Spatial Registration Tools for NIRS

Good resources for up-to-date information about fNIRS training opportunities are the newsletter of the Society for functional Near Infrared Spectroscopy and the Facebook page of the SfNIRS. The upcoming fNIRS2020 – Due to the ongoing COVID situation, the officers of SfNIRS, board of directors and organizers of fNIRS 2020 have taken the decision to postpone the conference for one whole year. fNIRS 2021 will now take place on 10-13^th October 2021 in the same venue at Boston University.

Different groups offer fNIRS courses and workshops throughout  the year (let us know of any others to include here):

• The Boston University NeuroPhotonics Center holds an annual 3-day fNIRS course run by David Boas and Meryem Yücel (previously hosted at the Martinos Center at Massachusetts General Hospital).
• Dr. Ted Huppert and lab at the University of Pittsburgh hosts a two-day intensive fNIRS training course on advanced data analysis and experimental design.
• Artinis has held a workshop in 2018.