MNE-NIRS: montage and plot_topo of GLM results

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1

Dear all,

  • MNE version: 1.6.1
  • MNE-NIRS version: 0.6.0
  • operating system: linux CentOS 7

I am trying to process old NIRx data.
I managed to convert the data from .nirs to .snirf format.

I created a montage from the optodes and fiducials locations I had (X, Y, Z coordinates in MNI space) using mne.channels.make_dig_montage and set_montage, and the position of the optodes looks correct when I use montage.plot():

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I then computed the haemoglobin data and solved a very simple GLM (it’s just a finger-tapping task alternating with rest). I tried to plot the GLM parameters using plot_topo(conditions=['Task'])
but the channel positions are not correct at all, I obtain such plots:

image

How can my custom montage be recognized by plot_topo()? I understand that plot_topo() needs a layout as input, not a montage, so how can I obtain a layout information from a custom montage?

Thanks in advance for your help
Melanie

2

Hei, can you please tell me how you converted the nirs to .snirf format?

3

mentioning an mne expert @rob-luke here. I am facing the same problem, would be great if you could help us out here and shed some light into this matter on why are the plots coming outside the head. In my case i am reading a .wl1 file

1 Like
4

I’m deeply sorry I took so long to answer. In fact I did not find any solution.

I ended up with reading directly the .nirs data using mne.io.read_raw_nirx and I did not have the registration problem any more. I did not use the .snirf format.