Neuropype: motor imagery tutorial, questions

Doc_SlaterDoc_Slater Colorado
edited February 2022 in Software

Greetings. I'm trying to motor imagery tutorial on the website using a Cyton. Using the GUI I can confirm there is EEG, and the LSL stream seems to be recognized. I went through the calibration to create the xdf file, and I edited the pipeline as specified in Neuropype. And the following happens:

Loading pipeline...
INFO: execution started
INFO: execution resuming
INFO: Importing XDF file C:/Recordings/CurrentStudy/exp1/slater1.xdf...
INFO: Imported file C:/Recordings/CurrentStudy/exp1/slater1.xdf.
INFO: Imported file C:/Recordings/CurrentStudy/exp1/slater1.xdf.
INFO: Resolving data stream (name='obci_eeg1')...
INFO: Applying FIR filter...
INFO: CSP model is training now...
****ERROR: The following error occurred in node Common Spatial Patterns: shape of data ((2, 4)) must match lengths of axes ((2, 6))****
WARNING: The channel labels of the given stream were missing or incomplete. Auto-generating labels.
INFO: LSL: Data stream obci_eeg1 acquired.
ERROR: CSP must be trained before it can be used

Honestly I'm not sure where to begin looking for the "Common Spatial Patterns" node to figure out why the data shape doesn't match the axes length. If I just run the pipeline without editing it (with no EEG input from my headset) it executes appropriately. Where should I start looking? Any suggestions will be appreciated. Thanks!

Comments

  • wjcroftwjcroft Mount Shasta, CA

    Doc, hi.

    So you are referencing this tutorial, by Rakesh Jakati, @Rakeshbci,

    https://docs.openbci.com/Examples/EEGProjects/MotorImagery/

    I've referenced, using the at-sign notation, Rakesh. Hopefully he will see your error and respond. Possibly also suggesting any edits to the tutorial to avoid users encountering this in the future.

    Regards, William

  • wjcroftwjcroft Mount Shasta, CA

    Mentioning @rakeshbci01, @Rakeshbci, can you please comment?

  • Hi,
    The pipeline on my computer is working fine. I am using NeuroPype Academic edition 2020.0.3, try using this version.
    I had another user with the same issue, but the error was due to not including the EEG markers in the stream. I will send you a .xdf to calibrate the pipeline, try using that before using live headset.

  • DevyanshDevyansh Brooklyn, New York
    edited December 2021

    Hello Doc,
    I would recommend you to go to the Pipeline Designer and select the CSP (Common Spatial Patterns) node and change parameter to 2.
    This should hopefully fix the issue.
    Regards
    Devyansh Gupta

  • wjcroftwjcroft Mount Shasta, CA

    @Doc_Slater, hi.

    Just checking on your situation. Did any of the comments by Devyansh or Rakesh solve your issue? Do you have a recommendation on how the current document could be improved?

    Thanks, William

  • OK, so it now works (sort of). So I'm using the ThinkPulse active electrodes from Conscious Labs. They work well, but do require that one lowers the PCA gain (via a command in the GUI). If I start the LSL stream via the GUI, then start the pipeline I get an error due to the channel labels being unrecognizable. I've tried to figure out how to change the labels within the GUI and thus far failed. However if I just run the GUI to send the needed hardware commands, start streaming the data so I can see it and fix any electrode contact issues, then STOP the stream, I can then open an anaconda python command window, run the openbci_lsl.py program, and pass the correct electrode labels on there. Then I start the LSL stream using the command line. ONLY then can I start the Neuropype pipeline and it works. I say sort of because the calibration file that Rakesh was kind enough to send doesn't work especially well (I'm sure because I'm using active instead of passive electrodes). Now that I know how to do the two-step to connect the board AND the electrode labels to software, I'll try rerunning to the python code to do my own calibration. My hope is that will work a bit better.
    I should emphasize the fact that without Rakesh's help and the file he sent, I never would have figured this out and gotten it to work at all, so he's my hero :smiley:

    Thank you all very much for the help!
    Doc

  • Hi! I'm trying to motor imagery tutorial on the website using a Cyton.

    I edited the pipeline as specified in Neuropype.

    And the following happens:

    graph loading graph structure
    graph saving graph structure
    graph loading graph structure
    resetting CPE instance...
    graph saving graph structure
    graph loading graph structure
    execution started
    execution resuming
    Resolving data stream (name='obci_eeg1')...
    Importing XDF file C:/Recordings/CurrentStudy/exp2/test.xdf...
    Imported file C:/Recordings/CurrentStudy/exp2/test.xdf.
    Imported file C:/Recordings/CurrentStudy/exp2/test.xdf.
    Applying FIR filter...
    CSP model is training now...
    Logistic Regression: now training...
    eeg: neuropype.engine.block.Block( data=(120, 2)array([[0.79973059, 0.20026941]; [0.48405832, 0.51594168]; [0.80936313, 0.19063687],... [0.36968697, 0.63031303]; [0.36025997, 0.63974003]; [0.35067485, 0.64932515]]), axes=["InstanceAxis(times=[1447.0862232569184, 1451.7770587225323, 1456.460429688201, 1461.1372103539177,...True, 117, 66), ('left', 0.0, True, 118, 51), ('left', 0.0, True, 119, 52)], instance_type='trial')", "FeatureAxis(names=['left', 'right'],;\tunits=['', ''],;\tproperties=[0, 0],;\terror_distrib=[0, 0],;\tsampling_distrib=[0, 0])"])
    LSL: Data stream obci_eeg1 acquired.
    The following error occurred in node LSL Input: argument of type 'NoneType' is not iterable
    The following error occurred in node LSL Input: argument of type 'NoneType' is not iterable
    The following error occurred in node LSL Input: argument of type 'NoneType' is not iterable
    

    The error occurs in the LSL input step. I have the following configuration:

    and in GUI:

    (I try others configurations and the same)

    Do you know what I'm doing wrong?
    Thanks!

  • wjcroftwjcroft Mount Shasta, CA

    Hi @arellanon,

    I've merged your new question on the Neuropype MI tutorial, into this existing thread. I am hoping that @Rakeshbci or @Devyansh can offer some suggestions. As they are experts on Neuropype and the tutorial was written by Rakesh.

    Regards, William

  • wjcroftwjcroft Mount Shasta, CA

    I am hoping that @Rakeshbci or @Devyansh can offer some suggestions. As they are experts on Neuropype and the tutorial was written by Rakesh.

    William

  • arellanonarellanon Argentina

    Hi! I try a basic Neuropype LSL input with all configurations in LSL input ( check Enable diagnostics, Proc clocksync.. etc)


    I get the same error

    LSL: Data stream obci_eeg1 acquired.
    The following error occurred in node LSL Input: argument of type 'NoneType' is not iterable
    The following error occurred in node LSL Input: argument of type 'NoneType' is not iterable
    The following error occurred in node LSL Input: argument of type 'NoneType' is not iterable
    

    In Neuropype I see active LSL

    I don't know that more modify.
    Thanks!

  • I follow the guide at "https://docs.openbci.com/Examples/EEGProjects/MotorImagery/",but when running the"SimpleMotorImagery.pyp",it went wrong and keep popping the"CSP must be trained before it can be used" ERROR.
    How should I do to fix this error?

  • wjcroftwjcroft Mount Shasta, CA

    @zealor187, hi.

    I merged your new thread into this existing thread on the same topic. Please read the previous comments and solutions.

    William

  • @wjcroft said:
    @zealor187, hi.

    I merged your new thread into this existing thread on the same topic. Please read the previous comments and solutions.

    William

    thank you sir

  • my error is because I want to make 4 classification task.I change the"motorimag_calibrate.py"script's label(in the line15) and makers(in the line 16) from 2 element list into 4 element list,and change some parameter and node in the pipeline designer.

  • @wjcroft said:
    @zealor187, hi.

    I merged your new thread into this existing thread on the same topic. Please read the previous comments and solutions.

    William

    I move the "motorimag_calibrate.py" script to the desktop because it is unchangeable in the original directory.
    and another problem is that the "lab recorder" didn't show the Marker stream.

  • wjcroftwjcroft Mount Shasta, CA

    @wjcroft said:
    I am hoping that @Rakeshbci or @Devyansh can offer some suggestions. As they are experts on Neuropype and the tutorial was written by Rakesh.

    William

  • @wjcroft said:

    @wjcroft said:
    I am hoping that @Rakeshbci or @Devyansh can offer some suggestions. As they are experts on Neuropype and the tutorial was written by Rakesh.

    William

    when I'm doing the 2 classification task, it can run,but still have the error "No non empty chunks with only_signals set to False found!" occur,and other error is: 1. ip 127.0.0.1 access denied; 2."Pipeline execution status" shows that "Calibrating" is False; 3.The Classification plot seems do not response to my real-time Motor Imagery.

  • wjcroftwjcroft Mount Shasta, CA

    I suggest you email Rakesh directly, and report his answer back here. His email is rakeshbci01 at gmail.com. He is the author of the tutorial. Not sure why he is not seeing the @Rakeshbci mentions.

  • JanuzJanuz Philippines

    Greetings. I'm following the motor imagery tutorial on the website using Neuropype and Cyton via this link: https://docs.openbci.com/Examples/EEGProjects/MotorImagery/. The EEG and the LSL stream seem to be recognized by the lab recorder and the motorimag_calib.py. I followed the tutorial step-by-step, from changing the CSP parameters to removing and replacing the required nodes. Yet after finishing the 10-minute training, and lab recording, I tried to start my pipeline and got the following error on my Neuropype log:

    graph loading graph structure
    graph saving graph structure
    graph loading graph structure
    graph saving graph structure
    execution started
    execution resuming
    Resolving data stream (name='obci_eeg1')
    Importing XDF file Jan132023CSPTraining1LeftRightArm.xdf
    Imported file Jan132023CSPTraining1LeftRightArm.xdf.
    Imported file Jan132023CSPTraining1LeftRightArm.xdf.
    Applying FIR filter...
    CSP model is training now...
    The following error occurred in node Common Spatial Patterns: Could not solve CSP problem. Your data might be rank deficient (e.g., not enough trials or electrically bridged channels). Try the FilterBankCommonSpatialPattern node with non-zero shrinkage.
    LSL: Data stream obci_eeg1 acquired.
    No non-empty chunks with only_signals set to False found!
    CSP must be trained before it can be used
    CSP must be trained before it can be used
    CSP must be trained before it can be used
    CSP must be trained before it can be used (statement loops)

    I'm wondering what the issue could be, and I'm hoping that some of you may have an idea of what I'm currently encountering. I posted some additional images as a reference.

    Thank you for taking the time to read my post.

  • wjcroftwjcroft Mount Shasta, CA
    edited January 13

    Hi @Januz,

    I've merged your new thread into this existing thread on the same subject. See some of the previous comments.

    In previous comments I have attempted several times to get a response from the tutorial author, Rakesh Jakati, @Rakeshbci. He has another username on this Forum also as @rakeshbci01. Neither of these has used the Forum since December 2021, according to our logs.

    He has not responded to users of his tutorial having issues. Here is his LinkedIn, perhaps you can try to contact him through that. Although in the past I've also messaged him there with no response.

    https://www.linkedin.com/in/rakesh-bci696933/

    I might suggest to Richard @retiutut, Eva @evaesteban or @Shirley that if users of Jakesh's tutorial are frequently stumped and cannot get a response from Rakesh, that this tutorial be labeled with a warning or deprecated so that OpenBCI users are not denied support with this tutorial.

    William

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