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Beginner Question- Creating SD struct using Atlas Viewer so I can convert NIRX file to nirs files.

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Katherine Boere
Posts: 6
Topic starter
(@katherineboere)
Active Member
Joined: 7 months ago

Hello all,

I am brand new to fNIRS- collection and analysis. I am currently running a combined fNIRS and EEG study, and attempting to process and analyze the data. I have searched the forum for this answer, but imagine it's so elementary that it isn't listed! My device is NIRsports2 with a frontal montage.

I am using MATLAB 2021b on a Windows laptop, Homer3 and Atlas Viewer, and want to use the NIRX2nirs converting function. It requires you to create an SD struct using Atlas Viewer prior to use and this is where I am struggling.

Below are the data files received from NIRx post-recording.


I then load the fNIRS file to Atlas Viewer, go to tools, probe and create/edit in SD. I get the following error.

Refpts: Found eeg system sphere file C:/Users/kathe/OneDrive/Documents/MATLAB/fNIRS/AtlasViewer/Refpts/10-5-System_Mastoids_EGI129.csd
fluenceProf0 = load('C:/Users/kathe/OneDrive/Documents/MATLAB/fNIRS/AtlasViewer/Data/Colin/fw/fluenceProf1.mat', 'index', '-mat');
load('C:/Users/kathe/OneDrive/Documents/MATLAB/fNIRS/AtlasViewer/Data/Colin/fw/fluenceProf1.mat')
Azimuth : 150.0
Elevation : 30.0
Orientation : LIA
Cam target : [128.0, 132.0, 130.0]
Cam old position : [110.7, 114.6, 3139.6]
Cam new position : [-1376.8, -1171.2, 2387.2]
Camera up vector : [-1.0, 0.0, 0.0]
View axis old : [17.3, 17.4, -3009.6]
View axis new : [1504.8, 1303.2, -2257.2]

Not enough input arguments.

Error in resetProbe (line 22)
resetProbe(probe, [dirname, dirs(ii).name], handles);

Error in AtlasViewerGUI>menuItemProbeCreate_Callback (line 3413)
atlasViewer.probe = resetProbe(atlasViewer.probe);

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in AtlasViewerGUI (line 19)
gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)AtlasViewerGUI('menuItemProbeCreate_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating Menu Callback.

Can anyone guide me in resolving this issue and moving forward?

Thank you!

5 Replies
Jennifer Keating
Posts: 4
(@jenkeats)
Active Member
Joined: 6 months ago

Hi, I'm having a similar error when trying to create/edit an SD file. Did you manage to solve this?

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Rob M
Posts: 20
(@rob-j-maclennan)
Eminent Member
Joined: 1 year ago

Hi Katherine, I'm also a beginner so don't know that I can help but maybe we could use more info. To my knowledge, the NIRSport2 creates .nirs files automatically. Are you trying to get the .nirs file type? Also, I see your screenshot and it looks like your system is creating different files from mine (I'm including a screenshot of my files). In the folder your NIRSport2 creates, can you click View > Details to get a column for the file type? 

 

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2 Replies
Katherine Boere
(@katherineboere)
Joined: 7 months ago

Active Member
Posts: 6

@rob-j-maclennan Thanks!

I figured it out, though. I just had to use the HomerOfflineConverter.m function provided by NIRx. Previously, I was using a different version.

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Rob M
(@rob-j-maclennan)
Joined: 1 year ago

Eminent Member
Posts: 20

@katherineboere You're welcome! Glad you figured it out.

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Sreekanth kura
Posts: 14
(@skurabu-edu)
Joined: 2 years ago

Hi Katherine,

If you still want to create SD file, can you try using AtlasViewer main branch instead of the released version. This issue was fixed in the main branch. 

Also, we recommend using newer probe design tool in AtlasViewer instead of SDgui. Here are the instructions  https://github.com/BUNPC/AtlasViewer/wiki/Designing-3D-Source-Detector-Geometry-in-AtlasViewer  to do that. 

But we will also make sure current version of the SDgui working properly without any errors.

Thanks,

Sreekanth

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