Error while running a BIDS dataset

koolgax99 commented 2 years ago

Me and my team are working on a dataset for research purposes, while running Automagic we ran into a error. The error is attached as follows. After much debugging we found that theres some issue in the read_brainvision_vhdr() function. The function is not able to read the data file.

System Specifications: Windows 10 Matlab 2022a Automagic v.2.6

The dataset which we are using is BIDS compliant and can be found here: OpenNeuro HD-EEGtask(Dataset 1)

The screenshot of the error:

The screenshot of the Automagic settings primarily:

Please help me with this error.

cc @ksgfan @nickilanger

ksgfan commented 2 years ago

Hi,

it seems that the fieldtrip function that is part of the old EEGLAB has some problems loading the BrainVision data.

You could go to the read_brainvision_vhdr.m and change line 69 info = dir(datafile); to info = dir(fullfile(p, '*sub*.eeg'));

The other option is to use development version of Automagic. We updated there all toolboxes, including EEGLAB.

Also, from what I see, you will get another error, because you don't specify channel location file. Browse to automagic-master/matlab_scripts/eeglab14_1_2b/plugins/dipfit2.3/standard_BESA/ and select standard-10-5-cap385.elp. Additionally, specify channel location file type: .besa.

The last hint - automagic recognizes BIDS format, so you could change Data Folder to .../research/hd_eeg_tracking. This way, all subject will be added to the project.

Best, Dawid

koolgax99 commented 2 years ago

Hi @ksgfan, Thanks for the wonderful answer, but still i am not getting the desired output.

The other option is to use development version of Automagic. We updated there all toolboxes, including EEGLAB. I am going ahead with this option. But there is a new error which Matlab is throwing and it can be seen in the ss attached below.

Also, from what I see, you will get another error, because you don't specify channel location file. Browse to automagic-master/matlab_scripts/eeglab14_1_2b/plugins/dipfit2.3/standard_BESA/ and select standard-10-5-cap385.elp. Additionally, specify channel location file type: .besa.

This suggestion asks me to specify the list of EOG channel indices in a comma or space separated format. Can you please tell me why this error persists?

The screenshot for the same is attached below

The last hint - automagic recognizes BIDS format, so you could change Data Folder to .../research/hd_eeg_tracking. This way, all subject will be added to the project.

Also i tried this too but somehow the Automagic is not detecting my eeg files and overdetecting the number of subjects. I have 23 subjects but it is showing 28 subjects. I have attached the screenshot for your reference.

Thankyou for your time. I really appreciate your help and work around AutoMagic.

ksgfan commented 2 years ago

File Extension should be still vhdr, not eeg

The error regarding EOG channels is probably due to EOG regression. If you want to perform EOG regression, you should specify EOG channels in the Configuration tab, just below the EOG regression tab(e.g. 10, 11, 23).

Number of subjects doesn't matter much, because folders without vhdr files will be skipped.

Let me know, if that helps.

koolgax99 commented 2 years ago

Hi @ksgfan,

I tried all the above configs, the Automagic is working now but it is throwing an error while preprocessing the data. This is the error i am getting right now in my matlab, after pressing he run button.

Processing file eeg_sub-01_ses-naming_run-1_eeg ...(file 1 out of 2)

ans =

    'Matrix dimensions must agree.'

Warning: Escaped character '\s' is not valid. See 'doc sprintf' for supported special characters. 
> In Project/writeToLog (line 1850)
In Project/preprocessAll (line 523)
In mainGUI>runpreprocessbutton_Callback (line 821)
In gui_mainfcn (line 95)
In mainGUI (line 61)
In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)mainGUI('runpreprocessbutton_Callback',hObject,eventdata,guidata(hObject))

1-a

Please help me solve it, thanks!!!

ksgfan commented 2 years ago

weird, because I tried preprocess your data and it works on my computer. Could you show me the main GUI window again? Additionally, could you go to script automagic/preprocessing/preprocess.m, set a breakpoint on line 143 and check, whether the data was loaded correctly? data should be a Matlab struct with the EEG.data field.

koolgax99 commented 2 years ago

hi @ksgfan

This is the main GUI of my Automagic.

However if its working in your computer can you please share your system specification for running it:

  - Matlab Version
  - EEGlab version
  - Automagic (dev or stable)
  - Other dependencies version

Thankyou so much for helping!!

ksgfan commented 2 years ago

Matlab 2020b EEGlab 2020_0 (it comes with automagic) Automagic developement

Also i am using a Mac OS 12.

But that shouldn't be a problem. Make sure that the data is not empty and that it is loaded properly.

koolgax99 commented 2 years ago

Hi @ksgfan I think i got where the issue is, it was because my data was not loaded properly. However, i still have a couple of minute errors. So, can we have a meet (Google Meet or Zoom Call) to help me debug those and also I wanted to know more about Automagic.

Thankyou, looking forward to hearing from you soon.

ksgfan commented 2 years ago

Yes sure. I am available almost the whole time. Please send me an e-mail with a date that fits you. dawid.strzelczyk@uzh.ch

methlabUZH / automagic

Error while running a BIDS dataset #58