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Questions about setting up for fNIRS analyses in Homer 3  


Jodie Gawryluk
Posts: 1
(@gawryluk)
New Member
Joined: 2 months ago

Thank you for offering the fNIRS workshop virtually this year, it has been very helpful in thinking about how to analyze our own data. Related to this, I have a couple of questions about analyzing a new data set in Homer 3. 

1. In one of the first sessions, it was mentioned that a probe file is needed. I noticed that when we open the data for the training exercises, different probe (source-detector) arrangements automatically come up. Is there a file that we should load to bring up the correct probe orientation for our own data or will this occur automatically as well? 

2. When setting up stim marks in the gui, it is clear to see how to label these for an individual run/participant. Is there a way to then apply the stim marks across all participants?

Thanks for your help!

Jodie 

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David Boas
Posts: 21
(@dboas)
Eminent Member
Joined: 2 months ago

In the exercises the probe geometry information was provided in the SNIRF file along with the fNIRS data. If you have your own data, you will need to get it into the SNIRF format with the SD probe geometry information. More and more vendors are supporting SNIRF. What system do you have data from?

 

Regarding question 2, there is no way to copy the stim marks between runs.

 

 

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1 Reply
Heather Kwan
(@hkwan)
Joined: 2 months ago

New Member
Posts: 3

@dboas We used a TechEn CW6 system, all the files automatically saved as .nirs files. 

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David Boas
Posts: 21
(@dboas)
Eminent Member
Joined: 2 months ago

@hkwan, the techen nirs file is the format that Homer originally used. The nirs file has the SD information and Homer3 will convert these nirs files to snirf files for you. You are all set! But you do know that the CW6 system needs you to provide these probe files before you acquire data. These are the same probe files that Homer3 expects in the snirf file and also that AtlasViewer uses.

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