fNIRS Course – DAY 2 – October 20, 2020

DAY 2 – October 20
10:00 am – 11:30 am ET

– Data analysis
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 – Basic steps demonstrated with Homer3 – LECTURE AND EXERCISE 

DAY 2 Video and Zoom chat:

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YILEI ZHENG (@zhengyilei)
1 day ago

Hi Abi,

For the second question, to exclude a stim mark from analysis, just drag the mouse over the mark and a dialog will appear. There would be a Toggle active On/off button. After clicking that button, the selected mark will be dashed in the StimEditGUI. This doesn’t delete the stim mark but only makes it excluded from the HRF calculation.
Hope this helps!

For the first question, I am sorry that I am actually not sure about that. Maybe let’s wait for answers from David or Meryem.


David Boas
David Boas (@dboas)
1 day ago

After you do what Yilei says, you then need to save the result back to the SNIRF file for it to affect the stim in Homer. If you don’t save this change back to the SNIRF file, then it will have no effect in Homer

Meredith Pecukonis
Meredith Pecukonis (@meredith)
1 day ago

adding David’s verbal explanation here for record keeping purposes:

solving GLM with Gaussian function (idxBasis=1) doesnt use stimulus duration information, so if you’re using this method you dont have to worry about duration of each stimulus/trial. Otherwise, you can enter different duration for each trial/stimulus and subject in stim GUI.

David Boas
David Boas (@dboas)
1 day ago

For the first question, Homer3 allows you to specify the stim duration for each block in the stimGUI. You can then decide whether or not to use this stim duration in the GLM as will be detailed in the GLM help and discussed elsewhere (hopefully on the wiki soon)

Lisa Bunker
Lisa Bunker (@lbunk)
1 day ago

Because of software issues, I am just barely catching up with day 1 and wasn’t able to ask questions in real time. For exercise 2, on the plot probe for the group data, when adding the tick marks, I assume that the first tick mark corresponds with the stimulus onset? And then the tick marks are every 5 seconds after that? (or whatever interval you set). Just wondering exactly what the reference is for where the tick marks start, as it looks to be shortly after the start of the HRF plot. Thanks!