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Different channels distance! using MNE and Brain AnalyzIR

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Posts: 6
Topic starter
(@hadi-borjkhani)
Active Member
Joined: 1 year ago

Dear FRESH community,

 

Thank you for making this FRESH challenge. Very helpful! Especially for those who develop toolboxes.

I am baffled about the channel's distance of Audio and Motor in FRESH data.

When I use MNE the distance of the channels is different than nirstoolbox. The problem is very critical and it is not about scale. The absolute values of the distances are different. Please see below:

First 7 Channels distances: Audio using MNE: I think the info provided by MNE is correct.

0.0359575
0.0359575
0.00815839
0.00815839
0.0305905
0.0305905
0.0307676
0.0307676
0.00756879
0.00756879
0.0341351
0.0341351
0.0340273
0.0340273

 

First 7 Channels distances: Audio using nirstoolbox:

20.4466363650974 ?
20.4466363650974 ?
8.11128257929257
8.11128257929257
15.2332194840217 ?
15.2332194840217 ?
10.0510025942323
10.0510025942323
7.56105199534823
7.56105199534823
32.5270976114536
32.5270976114536
33.1382655247028
33.1382655247028

 

I use "rawt = nirs.bids.loadBIDS([root_dir filesep 'FRESH-Audio']);" to load snirf data. But maybe I choose the wrong command to load .snirf data in nirstoolbox. But this command can load the data successfully.

Bests,

Hadi

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3 Replies
Posts: 6
Topic starter
(@hadi-borjkhani)
Active Member
Joined: 1 year ago

This problem was fixed temporarily. (MTALAB version 2019b)

The problem is in this recent version of Brain AnalyzIR after you load the .snirf, the Z coordinate of optodes will be zero in raw.probe.optodes. I think there are problems with functions that load the snirf data. 

Please do the following:

After you load the .snirf data, just insert the z coordinate of the source and detectors:

update the raw(i,1).probe.optodes.Z for source and detectors positions. You have to change it according to the optodes information in the .tsv file. for example in FRESH-Audio  "sub-01_ses-01_optodes.tsv" has the XYZ coordination of sources and detectors. 

I am sure that Ted will update his toolbox soon and this problem will be fixed. Or maybe this problem is because of the MATLAB version that I am using.

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Posts: 2
(@alinas)
New Member
Joined: 1 year ago

Hi Hadi,

Thanks for pointing this out, we ran into the same problem! After adding the Z coordinates, as you described, we now have the same optode distances in nirstoolbox as you get in mne.

Best regards from

Copenhagen fnirs crew

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Posts: 2
(@alinas)
New Member
Joined: 1 year ago

As Hadi described, it is only the coordinates for sources and detectors that we can find in the file. We noticed that the missing z coordinates of the landmarks still caused trouble for us when finding the correct corresponding EEG positions to each optode. It would help us a lot to have the ProbeInfo.mat file to derive an image of the montage. It doesn't exist in the BIDS format, does it? Is there any way to generate it from the files we got? 

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