Dear ERP experts,
I am trying to run dipole analysis using jack-knife option after I've run PCA in ERP toolkit.
For relevant background, we've run PCA analysis using ERP toolkit; our data comes from 128 EGI system and processed BVA tool.
After I successfully ran PCA analysis using ERP toolkit, we wanted to run a dipole analysis.
In the ERP toolkit, I press the Topos button and see topography from specific PCA factor combinations. Then, I right click in one of topography and press "jack-knife". Then, error pops up saying "Need at least three matching channel names to co-register the electrode cooridnates"
Anyone who can help me to fix this?
Any help and/or guidance would be very appreciated!
Many thanks!
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Sorry about the problem! The current EP Toolkit enhances electrode positioning by co-registering them with a canonical set of electrode positions via 10-5 names. The EGI system is an exception to this positioning system so my software has special procedures for handling them. They are recognized by EGI's standard practice of naming them E1-E128. Also, EGI mff files come with three fiducial points (nasion and two mastoids). I'm guessing that the pipeline through BVA discarded the fiducials and renamed the electrode channels. As a result, the EP Toolkit can't perform source analysis as it doesn't know where the electrodes are located. If you send me a copy of your file, I could provide more information and help you come up with a solution.
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Thank you for quick response!
Here, I've attached all 130 channels info. So when we did PCA in ERP toolkit, we used 128 channels, Cz and one pooling of three frontal sites from EGI system. so, the total number of electrodes are 130. The attached file is what I export .ced format to .excel format. Let me know if this is not what you are looking for!
Thanks!!
Just in case, I am also attaching other relevant file. This is what I used when running PCA in ERP toolkit.
Hope you can give us some insights to fix this!
Including Cz is fine. The reference channel is just another EEG channel so really I should have said 129 channels. Pooling the three frontal channels is a a little more problematic if you are double-counting some channels by including them in this extra 130th channel as well. Anyway, main problem is that my code won't recognize this as being EGI data if you have 130 channels rather than 129. My suggestion is to use the Edit function to reassign this 130th channel to being of type REG. This will inform EP Toolkit that this is not actually a channel of data but rather a combination of other channels and it will be ignored during analyses and it will stop confusing the co-registration code. Let me know if this solves your problem.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
I tried to attach one subject's .dat and. vhdr files. Are there files what you are looking for?
I wanted to attach .edf file but I couldn't. If you let me know your email address, I think that I can share .edf file with you through Duke Box. Just let me know!
Hi, Joe,
so, I tried to use "Edit" function as suggested but, when I changed "EEG to "REG" for the last 130th channel in the Edit, error pops up.. it seems like it doesn't read it correctly (see the attached)
Do you think there might be better solution to fix this?
Hi,
I ended up changing the 130th channel to "REG" in Edit function and ran PCA again. This time, I see that the 130th channel (i.e., pooling site) is not included in PCA analysis. Then, in the View, Topography function, I right clicked to check Jack knife option. but I face the same error that I had before.. At this point, I am stuck.. If you have any suggestions to fix this, would you please help me?
Many thanks!
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I fixed the error you ran into with the Edit function. I wasn't able to track down the problem with the jack-knife as you only sent me one subject average file. I need you to send me the actual spatial PCA file in .ept format that you are trying to jack-knife so I can reproduce your error exactly. You can use the Save function to create the .ept file.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi, Joe,
Great! Many thanks!
As suggested, I tried to attach .ept file but can't attach it as it is too large.
Can you let me know your email? Then, I can share the file with you. or email me at yusun.chung@duke.edu.
I really appreciate your help!!
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear ERP experts,
I am trying to run dipole analysis using jack-knife option after I've run PCA in ERP toolkit.
For relevant background, we've run PCA analysis using ERP toolkit; our data comes from 128 EGI system and processed BVA tool.
After I successfully ran PCA analysis using ERP toolkit, we wanted to run a dipole analysis.
In the ERP toolkit, I press the Topos button and see topography from specific PCA factor combinations. Then, I right click in one of topography and press "jack-knife". Then, error pops up saying "Need at least three matching channel names to co-register the electrode cooridnates"
Anyone who can help me to fix this?
Any help and/or guidance would be very appreciated!
Many thanks!
Sorry about the problem! The current EP Toolkit enhances electrode positioning by co-registering them with a canonical set of electrode positions via 10-5 names. The EGI system is an exception to this positioning system so my software has special procedures for handling them. They are recognized by EGI's standard practice of naming them E1-E128. Also, EGI mff files come with three fiducial points (nasion and two mastoids). I'm guessing that the pipeline through BVA discarded the fiducials and renamed the electrode channels. As a result, the EP Toolkit can't perform source analysis as it doesn't know where the electrodes are located. If you send me a copy of your file, I could provide more information and help you come up with a solution.
Thank you for quick response!
Here, I've attached all 130 channels info. So when we did PCA in ERP toolkit, we used 128 channels, Cz and one pooling of three frontal sites from EGI system. so, the total number of electrodes are 130. The attached file is what I export .ced format to .excel format. Let me know if this is not what you are looking for!
Thanks!!
Just in case, I am also attaching other relevant file. This is what I used when running PCA in ERP toolkit.
Hope you can give us some insights to fix this!
Including Cz is fine. The reference channel is just another EEG channel so really I should have said 129 channels. Pooling the three frontal channels is a a little more problematic if you are double-counting some channels by including them in this extra 130th channel as well. Anyway, main problem is that my code won't recognize this as being EGI data if you have 130 channels rather than 129. My suggestion is to use the Edit function to reassign this 130th channel to being of type REG. This will inform EP Toolkit that this is not actually a channel of data but rather a combination of other channels and it will be ignored during analyses and it will stop confusing the co-registration code. Let me know if this solves your problem.
I need to work out a better way of doing this. Could you send me a sample EEG file to go with the ced file you sent me for testing purposes?
Hi,
I tried to attach one subject's .dat and. vhdr files. Are there files what you are looking for?
I wanted to attach .edf file but I couldn't. If you let me know your email address, I think that I can share .edf file with you through Duke Box. Just let me know!
Last edit: Yu Sun 2021-01-23
Hi, Joe,
so, I tried to use "Edit" function as suggested but, when I changed "EEG to "REG" for the last 130th channel in the Edit, error pops up.. it seems like it doesn't read it correctly (see the attached)
Do you think there might be better solution to fix this?
Hi,
I ended up changing the 130th channel to "REG" in Edit function and ran PCA again. This time, I see that the 130th channel (i.e., pooling site) is not included in PCA analysis. Then, in the View, Topography function, I right clicked to check Jack knife option. but I face the same error that I had before.. At this point, I am stuck.. If you have any suggestions to fix this, would you please help me?
Many thanks!
I fixed the error you ran into with the Edit function. I wasn't able to track down the problem with the jack-knife as you only sent me one subject average file. I need you to send me the actual spatial PCA file in .ept format that you are trying to jack-knife so I can reproduce your error exactly. You can use the Save function to create the .ept file.
Hi, Joe,
Great! Many thanks!
As suggested, I tried to attach .ept file but can't attach it as it is too large.
Can you let me know your email? Then, I can share the file with you. or email me at yusun.chung@duke.edu.
I really appreciate your help!!