Re: [Erppcatoolkit-support] Using PARE correction for EEG data
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Re: [Erppcatoolkit-support] Using PARE correction for EEG data
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From: Maria T. W. <mtwijaya@u.nus.edu> - 2015-07-04 14:47:33
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Hi Joe, Yes I used EXG5 as the nose electrode. In addition to the 64 scalp electrodes, I used 8 external ones as follows: 65 - EXG1 - above left eye 66 - EXG2 - below left eye 67 - EXG3 - left mastoid 68 - EXG4 - beside right eye 69 - EXG5 - nose 70 - EXG6 - right mastoid 71 - EXG7 - left arm 72 - EXG8 - right arm Here's my processing pipeline up to the point where I generate the files I sent to you. Everything is done in EEGLAB 10 (Matlab 2010b). Nose-referenced files: 1. Import from bdf, referenced to EXG5, high pass filtered at 0.1 Hz, low pass filtered at 20 Hz. The command that I used for the referencing is EEG = pop_reref(EEG, [69],'keepref','on') 2. Manual rejection of non-typical artifacts 3. Removal of bad channels 4. ICA (runica) and removal of eye blinks and heart rate components 5. Interpolation of bad channels Average-referenced files: 1-3. same as above 4. Interpolation of bad channels 5. Re-reference to the average of 64 electrodes. The command that I used is EEG = pop_reref(EEG, [1:64], 'keepref','on') 6. ICA (runica) and removal of eye blinks and heart rate components Thank you. Regards, Maria ________________________________ From: Joseph Dien <jd...@ma...> Sent: Saturday, July 4, 2015 1:09 PM To: Maria Teresa Wijaya Cc: erp...@li... Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data I think I see. You used one of your external channels (EXG5) as a nose channel and then rereferenced to it? I need to know what EXG1-8 were used as in your dataset and what steps you took after data collection with respect to the reference to generate the two files (as in what software and what settings did you use). Thanks! Joe -------------------------------------------------------------------------------- Joseph Dien, PhD Research Associate Cognitive Neurology The Johns Hopkins University School of Medicine On Jul 3, 2015, at 9:31 PM, Joseph Dien <jd...@ma...<mailto:jd...@ma...>> wrote: Before I can address the PARE question, I’m having some trouble with your .set files. There is an aspect of them which is crashing my code. Could you tell me how the rereferencing was accomplished? To both nose and average reference? In particular, EXG5 is identified as being the reference electrode for the nose referenced dataset rather than CMS. Joe -------------------------------------------------------------------------------- Joseph Dien, PhD Research Associate Cognitive Neurology The Johns Hopkins University School of Medicine On Jun 28, 2015, at 10:16 PM, Maria Teresa Wijaya <mtwijaya@u.nus.edu<mailto:mtwijaya@u.nus.edu>> wrote: Yes, I did, sorry, I forgot about that. I've uploaded the files with the correct names in the folder: https://www.dropbox.com/sh/k2fpxx99kt6u0vg/AACpdOaLICsFdDBpLjollVWma?dl=0 Thank you. Maria ________________________________ From: Joseph Dien <jd...@ma...<mailto:jd...@ma...>> Sent: Monday, June 29, 2015 3:31 AM To: Maria Teresa Wijaya Cc: erp...@li...<mailto:erp...@li...> Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data I’m sorry, I can’t read the .set files you uploaded. It looks like you renamed the files? .set files don't let you do that. Could you send me the files with the original names? Joe On Jun 26, 2015, at 05:58, Maria Teresa Wijaya <mtwijaya@u.nus.edu<mailto:mtwijaya@u.nus.edu>> wrote: Hi Joe, I have uploaded the files to dropbox: https://www.dropbox.com/sh/k2fpxx99kt6u0vg/AACpdOaLICsFdDBpLjollVWma?dl=0 In my computer I could not load the ones with the event information so I removed the event information and stored them in the .csv file; these can be found in the "no event" folder. The files in the "with event" folder are from the same data set only with the event information intact. Thank you! Maria ________________________________ From: Joseph Dien <jd...@ma...<mailto:jd...@ma...>> Sent: Thursday, June 25, 2015 8:55 AM To: Maria Teresa Wijaya Cc: erp...@li...<mailto:erp...@li...> Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data How odd! Could you send me the nose-referenced and averaged-referenced data files so I can look into this? Joe On Jun 23, 2015, at 08:08, Maria Teresa Wijaya <mtwijaya@u.nus.edu<mailto:mtwijaya@u.nus.edu>> wrote: Dear Joe, Thank you for your quick reply. I have actually tried applying the PARE referencing to both nose-referenced and average-referenced data. In the former, it barely made any noticeable difference while in the latter it did change the grand average waveform. I am not sure why it did not work on the nose-referenced data. Is it actually okay to apply PARE referencing to a data set that has already been referenced to the average of the scalp electrodes? Thank you. Regards, Maria ________________________________ From: Joseph Dien <jd...@ma...<mailto:jd...@ma...>> Sent: Friday, June 19, 2015 9:27 PM To: Maria Teresa Wijaya Cc: erp...@li...<mailto:erp...@li...> Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data Thanks! You do not need to re-reference first. The PARE option is just a modified average-reference procedure (referenced to the average of the full interpolated head rather than just the average of the electrode locations). Use the “re-reference” option in the Topomaps view to get a sense of what it is doing. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, PhD Research Associate Cognitive Neurology/Neuropsychology The Johns Hopkins University School of Medicine On Jun 19, 2015, at 01:18, Maria Teresa Wijaya <mtwijaya@u.nus.edu<mailto:mtwijaya@u.nus.edu>> wrote: Hello, First of all, thank you for the amazing EP toolkit. I am currently trying to make use of the PARE correction feature. My data were recorded in Biosemi (64 channels) and have been filtered and re-referenced to nose in EEGLAB. My question is, do I have to first re-reference my data to average before using the PARE correction? Thank you and apologize if this question is too basic. Regards, Maria ------------------------------------------------------------------------------ _______________________________________________ Erppcatoolkit-support mailing list Erp...@li...<mailto:Erp...@li...> https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support -------------------------------------------------------------------------------- Joseph Dien, PhD Research Associate Cognitive Neurology/Neuropsychology The Johns Hopkins University School of Medicine -------------------------------------------------------------------------------- Joseph Dien, PhD Research Associate Cognitive Neurology/Neuropsychology The Johns Hopkins University School of Medicine ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. 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