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Problem with adding stim marks

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Sarthak Kohli
Posts: 5
Topic starter
(@sarthak99)
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Joined: 1 year ago

Hello,

 

I am having difficulty adding the stimulation marks in the StimGUI. After clicking on "edit stimulus" the pop up of StimGUI does appear and I am able to manually input time for stimulation marks but nothing gets generated on the file after I add a condition. I tried to check preview and I can see the stimulation marks in dotted lines along with the triggers (PortaSync) that I used during data collection. There's a lot a function in the StimGUI to "Generate 33 stim marks", this does not seem to work either. Is there something I am missing to add the stim marks? I have attached screenshots below for reference. The data was recorded using PortaLite from Artinis and the triggers are added using PortaSync. 


 



7 Replies
David Boas
Posts: 238
(@dboas)
Reputable Member
Joined: 2 years ago

it is not clear from this which version of Homer you are using. This was all working in the past. I believe that Stephen Tucker (@sstucker) has been making some updates to move us towards being compliant with BIDS-fNIRS in the development version. This can introduce these errors, maybe. Maybe this propagated into the master version. Maybe he can chime in on this issue?

But please confirm which version you are using.

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Sarthak Kohli
Posts: 5
Topic starter
(@sarthak99)
Active Member
Joined: 1 year ago

Hi Dr. Boas, thank you for your reply. I am currently using v1.33.0, R2017b and my colleague Siying has been using v1.33.0 R2021a (experiencing the same issue). 

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Stephen Tucker
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(@sstucker)
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Posts: 52

@sarthak99 It is probably a SNIRF file format issue if your colleague was able to reproduce it in a different MATLAB version. If you send a SNIRF file I can investigate further.

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Sarthak Kohli
(@sarthak99)
Joined: 1 year ago

Active Member
Posts: 5

@sstucker Hello Stephen, thank you for your reply. Me and my colleague were having the same issues using different Homer3 versions. I am unable to attach the snirf files here (gives me an error) I have sent you the files over email.

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Sarthak Kohli
(@sarthak99)
Joined: 1 year ago

Active Member
Posts: 5

@sstucker Hello Stephen, I'm not sure if you received my email. I have uploaded the snirf files to a google drive folder. Here is the link: https://drive.google.com/drive/folders/1OthIl2-qqZ_5-myAMlMLsT0UC1lHEKdB?usp=sharing

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Sarthak Kohli
(@sarthak99)
Joined: 1 year ago

Active Member
Posts: 5

@sstucker Hey Stephen! Just following up on my previous query. Please let me know if you have any more information. Thank you!

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Emeline Mullier
Posts: 3
(@emullier)
New Member
Joined: 1 year ago

Hi Sarthak and Stephen,

I don't know if it helps but I have the same issue. I am creating my own .snirf file from raw data with 2 different scripts one matlab based and one python based.
If I create first a .nirs and then use the nirs2snirf function from Homer3 from matlab, I can open it in Homer without issue, see my aux and generate the stim marks with Homer (I just have this issue when i try to open the file in python with pysnirf2 https://openfnirs.org/community/data-forum/conversion-and-validation-of-nirs-to-snirf-files/ )

If I create my file with pysnirf2 based script, I can open the file in Homer3 (compiled exe version), visualize the aux exactly like you Sarthak but not generate the stim marks or add manual stim mark (but my file passes the validateSnirf from pysnirf2)

I can't understand why though. seems to me to be a different of string format between python and matlab but i don't know understand why it would affect the stim mark generation

 

Hope it helps

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