fNIRS Resource Manual
Manual Overview
The aim of this manual is to help new fNIRS users navigate the fNIRS project set-up and data collection process. This open-source manual will serve as a platform for other fNIRS users to share tips and resources with fellow fNIRS researchers.
This manual focuses on the utility of NIRX's NIRSport2 system.
What is fNIRS?
Functional near infrared spectroscopy (fNIRS) has been increasingly popular optical neuroimaging technique as it has shown to be a feasible method for studying the connections of cortical activation locations and behavior, as well as the neurodevelopment of children, due to its portability, tolerance to motion, and lower cost (Lloyd-Fox et al., 2010).
fNIRS measures brain activation using the near infrared spectra range to detect the hemodynamic concentration within cortical brain areas (Ferrari and Quaresima, 2012). The emission of NIRS from an object depends on the objects spectral window that allows light energy to absorb, then emit radiation energy, a process known as absorption spectra (Nilapwar et al., 2011). Human tissue and hemoglobin exhibit an absorption peak within the Near-infrared infrared range (780 nm to 1300 nm), which is what allows the fNIRS light source to travel through the cortex and detect the volume of oxygenated and deoxygenated blood (Jobsis, 1977).
On NIRX's Support website there is a great introductory video on fNIRS that we recommend you watch before working through the rest of this manual. The video is linked to the right. You will need to log into the NIRX Support to view.
Lloyd-Fox et al, 2010
NIRX NIRSport2 Device
NIRX has many resources on their website with guides and videos ranging from getting started with fNIRS to to data analysis. Click on the NIRX icon to access the NIRX support website, a username and password is required to access all materials.
Resources
Below are some of NIRX's resource highlights. All resources mentioned and more can be found on the NIRX Support Website.
NIRX fNIRS Equipment
NIRX Starter Kit Video
NIRX Cap Kit Video
NIRSport2 User guide
NIRScout User guide
NIRX has Independent Training Materials that are split up into modules that introduces users to fNIRS, fNIRS data acquisition, and data analysis: support.nirx.de/independent-training-materials
Click here to read NIRX's Software Installation Guide
Aurora fNIRS Acquisition Software: This is the acquisition application that you will need for the NIRSport2 if you are not using any NIRX short channel detectors.
NIRSITE Montage Software: This software allows you to create your cap configuration and export it to your acquisition file.
nirsLAB: This NIRX's data analysis software. It has two versions one that is stand alone and one that requires MATLab.
fOLD: This software allows you to choose your optode placement based on anatomical location. fOLD has a standalone software version and a MATLab version available for download.
Cap Configuration
fOLD: Optode Location Decider Tutorials
At this stage of your fNIRS experiment set up, hopefully, you have an idea of what brain regions of interest you would like to analyze in your fNIRS study. fOLD is a software that will allow you to see where sources and detectors should be placed on your fNIRS cap to cover the brain regions of interest. The video and PowerPoint below provide instruction on how to use the software.
fOLD: Optode Location Decider
Step 1: Download fOLD.
Step 2: Once fOLD is downloaded, decide which anatomical locations your optodes will cover.
Step 3: You may adjust the specificity of the brain area.
Step 4: Save or Export your location decider as a text file or an excel file. This will be your guide for creating your Montage on NIRSite software. To import it directly into NIRSite, export as a text file.
NIRSite: Creating a Montage
The video below on the left gives a brief overview on how to use the NIRSite Montage software. The video on right is is a DEN Lab video walking through how the DEN used NIRSite to build cap configurations.
For additional instruction, the NIRX support website, offers a "Getting Started PDF" and "NIRSite User Manual".
Building the fNIRS Cap
Supplemental Resource for Cap Building
These slides have location names for each of the slits in the adult 10/5 NIRX caps.
Also included in these slides is the NIRX Montage Editor Standard labels. This shows all of the locations that have slits on the cap
Symbol on Cap "X" = Red circles on the NIRX Montage Editor Standard labels
The dot symbol on the cap = the black outlines circles on the NIRX Montage Editor Standard labels
The yellow circles on the cap = the yellow circles on the NIRX Montage Editor Standard labels
The blue squares on the cap photos are not a part of the 10/5 layout but are locations that are found on the NIRSite montage software. Put this in building
Data Acquisition
Populating the Cap
Tips
If you are doing multiple fNIRS studies, clearly label the which cap sizes and configurations go with which study. The DEN Lab does this by labeling the bags that store the caps.
Create a plan so that you can populate your cap before your participant arrives, especially when working with children.
If you have more than one set of fibers, populate multiple caps sizes that fall within the average circumference of your population of interest. Use the appropriate cap size after you measure your participants head circumference.
Ideally, it would be nice to have the participant measure their head before they come to do the fNIRS study.
The DEN Lab has decided not to clean the caps or fibers in between study visits. Any alcohol solution can damage the equipment.
Connecting Wirelessly
Connecting a Single NIRSport2 8X8 Device
Click here for a step-by-step protocol.
Hyperscanning
Click here for a step-by-step protocol
fNIRS Signal Optimization and Troubleshooting
Click here to view the NIRX Aurora Manual
Additional NIRX Resource Videos for Connecting the NIRSport2
Connecting the NIRSport 2 Device
The DEN Lab uses an access point to connect NIRSport2 devices to Aurora.
Here is a link to NIRX's Connecting to an Access Point instructions: https://support.nirx.de/archives/knowledge/how-do-i-connect-my-nirsport-2-to-an-access-point
Hyperscanning with Nirsport2
This Hyperscanning video can also be found on NIRX's website. The DEN Lab in-house protocol to establish connection for hyperscanning projects can be found below.
Data Quality
For another resource on data acquisition, follow this link to NIRX's website: ShareFile - Where Companies Connect
DEN Lab fNIRS Materials
HSCAN_Logbook_Sheet.docxDEN fNIRS Log Sheet
fNIRS Shopping List (AutoRecovered).docxfNIRS Shopping List
HSCAN Checklist.docxDEN fNIRS Study Checklist
HSCAN Protocol_Ying.docxDEN Lab fNIRS Study Protocol Example
General fNIRS IRB Language.docxGeneral fNIRS IRB Language
