Software

This page will provide links to software developed for use in fNIRS imaging. Please contact us with any additions or changes.


fNIRSOFT

fNIRSOFT is stand-alone software to process, analyze and visualize functional near infrared (fNIR) spectroscopy signals through a graphical user interface and/or scripting (for automation), distributed by BIOPAC Systems, Inc. and developed by fNIR Devices.


fOSA-SPM

fOSA is a software package for the processing and analysis of functional neuroimaging data using Near Infrared Spectroscopy (NIRS). The software description and operation manual is provided in the package. The current version of the software is 2.2.


fc-NIRS

fc-NIRS is an analysis tool for functional connectivity(fc)and brain network calculation. It includes the main functions of fNIRS data quality control, data preprocessing, FC calculation, and graph-theory based network analysis. fc-NIRS 2.0 has been released by Haijing Niu on May 2019. It can be freely downloaded at https://www.nitrc.org/projects/fcnirs.


fOLD

This toolbox allows for optode arrangement based on anatomical landmarks based on five parcellation methods. Alternatively, one can also load volumetric fMRI data (NIfTI or ANALYZE) as mask for the fNIRS optodes positions.


HOMER3

HOMER3 is the next evolution of the Homer GUI for analyzing fNIRS data. It expands on Homer2 by allowing for custom processing streams at the session and group levels. It also incorporates the SNIRF data format. Underneath the GUI, all of the processing functions can be accessed at the script level, adding additional flexibility. Users are encouraged to contribute their own scripts for public dissemination within HOMER3. AtlasViewer is now also available through GitHub as well.


HOMER2

HOMER2 has a GUI interface similar to HOMER1, but now more easily supports group analyses and re-configuration of the processing stream. Further, it enables users to integrate their own algorithms into the processing stream. Underneath the GUI, all of the processing functions can be accessed at the script level, adding additional flexibility. Users are encouraged to contribute their own scripts for public dissemination within HOMER2.


Imperial College Near Infrared Spectroscopy Neuroimaging Analysis (ICNNA)

Imperial College Near Infrared Spectroscopy Neuroimaging Analysis (ICNNA), previously known as Imperial College Neuroimage Analysis (ICNA), is a Matlab-based analysis tool for fNIRS neuroimaging data. In contrast with other software tools such as HomER or fOSA, it places the emphasis on the analysis over the processing with the experimnent instead of the individual neuroimage being the central piece of information. It has statistical, topological and graph-theory based capabilities.


NAP

NAP is a MATLAB-based analysis package developed and custom-tailored for analysis of NIRS data, either through a GUI or through the command line. It enables signal denoising and GLM analysis, as well as anatomical registration of the measurements. NAP enables the analysis of entire data sets with a few button clicks.


Neuroimaging Tools and Resource Center

The Neuroimaging Tools and Resource Center is a large repository of tools and resources serving the broad neuroimaging community.


NIRFAST
Open source software for multi-modal optical molecular imaging. Includes image segmentation, multimodal optical modeling (continuous-wave, time-domain, frequency-domain), parametric image reconstruction and overlay visualization.


NIRSLab

NIRSLab is a versatile opensource software package designed for complete fNIRS data analysis with modules for data registration, preprocessing, hemodynamic state visualization with 3D projection, and GLM offering signal extraction with SPM and headspace modeling. It accepts various file formats, and can be used with 3rd party devices.


NIRSite

NIRx’s easy to use MNI based montage creator, NIRSite, offers manual and importation of coordinates for registration and digitization in both 2D and 3D planes. Provisions include automatic channel assignment and short channel support, with effortless export to either acquisition platform; Aurora or NIRStar.


NIRS-SPM

NIRS-SPM is an SPM5– and MATLAB-based software package for statistical analysis of near-infrared spectroscopy (NIRS) signals. It was developed at the Bio Imaging Signal Processing (BISP) lab at KAIST in Korea.

 A new NIRS-SPM toolbox update has been released by Sungho Tak on September 2015. It is freely available for download.


NIRStorm

Brainstorm plugin for fNIRS data analysis.


NIRx NIRSlab

NIRSLab is a versatile opensource software package designed for complete fNIRS data analysis with modules for data registration, preprocessing, hemodynamic state visualization with 3D projection, and GLM offering signal extraction with SPM and headspace modeling. It accepts various file formats, and can be used with 3rd party devices.


NIRS Toolbox

Ted Huppert and Jeff Barker have released a new Matlab-based toolbox for fNIRS. The toolbox incorporates all of the lab’s newest innovations including statistical analysis methods for single subject and group level models, mixed effects and ANOVA models, image reconstruction, and functional connectivity analysis. Training videos recorded at the 2018 AnalyzIR Workshop are available at: huppertlab.net


MCX/MMC
Open-source, GPU-accelerated software for simulation of photon migration in 3D modeled turbid media.


Open PoTATo

Open PoTATo (Open Platform of Transparent Analysis Tools for fnirs) is a platform software for fNIRS data analysis on MATLAB, which was developed by Hitachi and carried over by AIST as an MIT licensed open source version. It equips with a GUI-based workbench for exploring data analysis methods and sharing analysis recipes among users. It is freely available to all fNIRS users, from beginner to experts.


PHOEBE

PHOEBE  (Placing Headgear Optodes Efficiently Before Experimenting) is a graphical software that measures and displays, in real time, the optical coupling between fNIRS optodes and the scalp of a subject. The primary goal of PHOEBE is to help optimizing the placement of an fNIRS headgear in terms of both time efficiency and signal quality. Download, manual and support available at: https://bitbucket.org/lpollonini/phoebe/wiki/Homehttp://www.uh.edu/tech/pollonini/phoebe/


SNIRF – Shared NIRS Data Format

SNIRF is designed by the community in an effort to facilitate sharing and analysis of NIRS data.


Spatial Registration Tools for NIRS

The Functional Brain Science Lab at Jichi Medical University is dedicated to the technical development of spatial registration for NIRS. A variety of tools are described on the lab’s website.


Turbo Satori

By Brain Innovation: a highly-flexible real-time analysis package for the NIRx NIRSport (v. 1 or 2) or NIRScout systems. Includes signal quality, 3-D and 2-D views, connectivity/coherence, built-in neurofeedback & BCI protocols/examples, short channel regression, block averages (incl. error bars), T-Stat, & GLM analysis (SPM-based): customizable HRF, Betas, condition contrasts, time to peak/undershoot, etc.