Visualizing .snirf linked file

[aeddins22]

Hi Raymundo,

I just updated Brainstorm today, but I am having similar challenges importing the .snirf file from NIRSport2 Aurora software. Two main errors -

1. After selecting review the raw file, I right click to display the sensors (either scalp or pairs) and Matlab throws an error related to the view_channels function, not enough input arguments. I am able to see them when viewing via the NIRS > 3D optodes option.
2. When I display the raw time series, it only shows single responses (in black) but does not break them out by frequency.

Any suggestions?
Thank you!
Ann

[Raymundo.Cassani]

Hi @aeddins22,

@aeddins22

1. After selecting review the raw file, I right click to display the sensors (either scalp or pairs) and Matlab throws an error related to the view_channels function, not enough input

This suggests that the not scalp surface for that Subject. Probably this Subject is not using the Default anatomy and the anatomy is not imported.

@aeddins22

2. When I display the raw time series, it only shows single responses (in black) but does not break them out by frequency.

Did you set the montage to: NIRS Overlay?

From the NIRS tutorial:

If coloring is not visible, right-click on the figure the select "Montage > NIRS Overlay > NIRS Overlay"

If you are new using NIRS in Brainstorm, we suggest you to follow the NIRS tutorial with the provided data to get familiar with the options for NIRS.

https://neuroimage.usc.edu/brainstorm/Tutorials/NIRSFingerTapping

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P.S. These questions were moved to their own, as they were not related to the other thread

[aeddins22]

Thank you so much for the quick reply! For the anatomy, I do not have anatomy to import for each individual, other than the digipts.txt file from Aurora. I was following the tutorial which suggested leaving that option as "No, use individual anatomy", but maybe I should try using default instead. Thanks for the pointer on changing the image colors! I have been using Brainstorm with EEG for over 10 years but feel like I'm on a new learning curve using it with NIRS. I'll keep referring to the tutorial for guidance. Thanks again!

[Raymundo.Cassani]

@aeddins22

but maybe I should try using default instead

Yes, default anatomy is better that none :P

@aeddins22

Thanks for the pointer on changing the image colors! I have been using Brainstorm with EEG for over 10 years but feel like I'm on a new learning curve using it with NIRS.

That's nice! Please let us know any feedback on that and any other tutorial