NIRSTORM / Import MNI coordinates for channels projection

[brieucleger1999]

Hello everyone, i hope that you are doing well !

I'm using two devices from Artinis MS, Brite MKII and Brite MKIII.
In order to have a good look of my channels on the scalp (and with the future idea of generating a sensitivity maap), i used a Polhemus Fastrack to digitize my optodes. This was done in the Oxysoft software provided by Artinis MS. This results in a .xlsx file which look like this :

Then, i would like to import these coordinates in NIRSTORM using the Colin27 4 NIRS template (or another if preferable) but i can't find a way to do it. So i tried to manually change it with "Edit channel file", that works but does not fit the MRI template. I can't provide a screenshot because I deleted it by accident but i saved it in a .pos file (but when i try to import this file with "Add EEG positions", it does not change the coordinates) :
channel.pos (2 Bytes)

I also found a similar discussion but it had no solution : How to import the MNI probe coordinate of NIRS into brainstorm?

What should I do ? Is there a tutorial that I missed or that I did not understand ? In the NIRS finger tapping tutorial, the coordinates are provided with Brainsight but both fiducials and optodes txt are not "written" as mines.

Thank you very much for your help,
Kind regards,
Brieuc

[edelaire]

Hi.

it seems tha the pos file is empty. i would suggest to have a look at the bids suggestion to format the nirs coordinate: Near-Infrared Spectroscopy - Brain Imaging Data Structure 1.10.0

Here is an example:
sub-01_task-tapping_run-01_optodes.tsv (656 Bytes)

Note that you will have to rename Rx1 to D1 and Tx1 to S1.

You will then be able to import the coordinate using 'add EEG position > import from file > using the file format : EEG: BIDS electrodes.tsv mni space (mm) (*.tsv)

[brieucleger1999]

Hi Edouard, sorry for the delayed response.

So i tried to project channels as you explained by writing my optodes coordinates in a .tsv :
coord_nirstorm.tsv (1.2 KB)

I finally manage to make it work, i had issues with the Colin27_4NIRS template.

With my .nirs, i just saw a problem when i display the projection on the figure, dorsal :

When looking at the frontal channels (image below), we can see that there is no problem on the (real) left side but on the right side, bad links (channels) can be seen. Links should have been made between S17-D13 / S20-D14 and S16-D14 and there should be no links between S20-D13 / S16-D13 and S17-D14. Thus, it would be symmetrical and it should be.

How can i solve this problem ?

I also tried with the same data in the snirf format and when trying to import the coordinates (Add EEG positions), i get this error :

Index exceeds the number of array elements. Index must not exceed 0.

Error in channel_add_loc (line 116)
idef = find(strcmpi(sprintf('S%s', toks{1}{1}) , locChanNames));

Error in tree_callbacks>@(h,ev)channel_add_loc(iAllStudies,,1) (line 2896)
gui_component('MenuItem', jMenu, , 'Import from file', IconLoader.ICON_CHANNEL, , @(h,ev)channel_add_loc(iAllStudies, , 1));

Much thanks for your answers,
Brieuc

[brieucleger1999]

Hello Edouard,

I manage to make it work, i had switched D13 and D14 in the file.

For the snirf part, the problem remains the same. I will work on the .nirs for now.

Thank you very much !

Brieuc

[edelaire]

great.

I should have time to look at the snirf at the end of the week. but yeah if the nirs file is working I would recommend working with that.

How was the snirf file generated ?

[brieucleger1999]

Thank you very much ! No worries i'm working with nirs files right now

As i recorded with Artinis MS devices, Brite MKII / III, data are stored as .oxy5 files. Then, Artinis MS provides a .mat "Oxysoft2matlab" to convert .oxy5 in various types with the option to convert it in .nirs or .snirf.
So both files should contain the same data !

See you soon !
Brieuc