[Eeglablist] [External] Re: Eeglablist STUDY error: Dataset concatenation

Wed Mar 4 06:26:13 PST 2020

Hello Paul,
I recommend you try creating a study with just one data set and see if that
works. If that works, you add in another data set collected with the same
EEG system and check again. If that works, then add in one other data file
collected with the other EEG system.  If the error appears, then it's
because of the two different channel location files associated with each
set of files you have.

You may need to reprocess half the files to be sure that the channel locs
file (the .ced etc..) are identical for all files from the first stages of
processing.

Kathleen Van Benthem Ph.D., Senior Research Scientist
Advanced Cognitive Engineering Laboratory

Institute of Cognitive Science

Carleton University, Ottawa, ON. Canada. K1S5B6

kathy.vanbenthem at carleton.ca

Phone:  (613) 520-2600 Ext:2487

On Wed, Mar 4, 2020 at 3:08 AM Beach, Paul Anthony <
paul.anthony.beach at emory.edu> wrote:

> [External Email]
>
> I tried downloading 2019b and running channel pre-computation. Same exact
> errors at the same spots. :-/
>
> Does anyone have any suggestions regarding the errors for eeg_getdatact
> (line 111 and 113)?
>
> Thanks!
>
> On Mar 3, 2020, at 12:09 PM, John Johnson <john.johnson at gatech.edu<mailto:
> john.johnson at gatech.edu>> wrote:
>
>
> Hi Paul,
>
> I wonder if this as a compatibility issue with MATLAB 2019a.
> I just had problems plotting channel measures with similar error text when
> running my study on my laptop running Matlab 2019a. The same study runs
> fine on my computer at home which runs 2019b.
>
> Your error:
>
> EEGLab error in function eeg_getdatact() at line 113:
> Unable to perform assignment because the size of the left side is
> 72-by-256-by-438 and the size of the right side is 80-256-by-438.
>
> My error can be seen here:
> https://github.com/sccn/eeglab/issues/137
>
> Perhaps they share a Matlab function that is causing the assignment error
> in both.
>
> Regards,
> John
>
> John T. Johnson
> PhD Candidate - Cognitive Motor Control Laboratory
> Lab TA NEURO 3010 Neuroscience Methods
> School of Biological Sciences
> Georgia Institute of Technology
> john.johnson at gatech.edu<mailto:john.johnson at gatech.edu>
> he/him/his
>
> On 3 Mar 2020, at 11:34, Beach, Paul Anthony wrote:
>
> Hi John - thanks again for the reply.
>
> I did attempt interpolation as part of my single subject pre-processing
> stream using the method endorsed by Makoto before/after use of ASR:
>
> In case helpful, my basic pre-processing steps (using Biosemi 64ch EEG)
> are:
> Import w/ mastoid reference
> Down sample to 256
> Baseline removal -> FIR filtering (0.5 and 50 Hz) -> Import channel locs
> Cleanline -> Makoto’s step for retaining full channels: originalEEG = EEG;
> ASR (with pre-post steps outlined above)
> Interpolation using Makoto’s step: EEG = pop_interp(EEG,
> originalEEG.chanlocs, 'spherical');
> Avg referencing
> Cardiac event marking (R and T waves) and use of ERPLAB to create
> bin-based epochs
> ICA with ‘pca’ keep option and # channels remaining after ASR to protect
> RANK
> DIPFIT/Bilateral dipole fitting
>
> I will say that, while I include every channel in my pre-processing steps
> with respect to filtering/clean line/ASR, I do exclude from my Avg
> referencing all non-EEG ancillary channels (e.g mastoid, ECG or others).
>
> Any chance any of the above steps could be causing problems (including my
> mentioned one) for group analysis?
>
> In either case I’m not sure how to go down to the ‘common denominator’ in
> using just the bare 64 channels with respect to STUDY creation. I’d love
> some suggestions to try.
>
> Thanks!
> Paul
>
>
> On Mar 2, 2020, at 8:40 PM, Johnson, John T. <john.johnson at gatech.edu
> <mailto:john.johnson at gatech.edu><mailto:john.johnson at gatech.edu>> wrote:
>
> Hm. The 72 or 80 channels make me wonder if perhaps it’s problem with
> channel locations - maybe the other channels can’t be interpolated. Or
> perhaps the rank of the data is too low to create new channels.
> I suppose a last resort would be to use the lowest common denominator and
> go with the minimum number of channels.
>
> Sent from my iPhone
>
> On Mar 2, 2020, at 8:17 PM, Beach, Paul Anthony <
> paul.anthony.beach at emory.edu<mailto:paul.anthony.beach at emory.edu><mailto:
> paul.anthony.beach at emory.edu>> wrote:
>
> 
> Thanks for the response, John.
>
> I tried changing the version to that which is currently on GitHub
> (2019.1). I still am getting the same error at the same spot. I know it has
> to have something to do with the ERP pre-computation because if I don’t
> select it and, for example, just choose ‘power spectrum’ then it completes
> the task. I’m not really sure where the error would be coming from, though.
>
> Taking out the line in question in the eeg_getdatact.m script (line 111)
> and then trying to repeat the process of channel pre-computation I get this:
>
> EEGLab error in function eeg_getdatact() at line 113:
> Unable to perform assignment because the size of the left side is
> 72-by-256-by-438 and the size of the right side is 80-256-by-438.
>
> I’m not really sure what to do about this. Yes, some of my subjects’ data
> were collected with a different number of channels (some 72, some 80, using
> peripheral Biosemi channels). It seems like EEGlab should be able to
> function irrespective of this.
>
>
> Cheers,
> Paul
>
> On Mar 2, 2020, at 6:22 PM, John Johnson <john.johnson at gatech.edu<mailto:
> john.johnson at gatech.edu><mailto:john.johnson at gatech.edu>> wrote:
>
>
> Have you tried using a non-develop branch of eeglab?
> Develop branches are generally more volatile and prone to bugs that
> release branches.
>
> https://github.com/sccn/eeglab/tree/eeglab2019.1
>
> John T. Johnson
> PhD Candidate - Cognitive Motor Control Laboratory
> Lab TA NEURO 3010 Neuroscience Methods
> School of Biological Sciences
> Georgia Institute of Technology
> 678-575-2093
> john.johnson at gatech.edu<mailto:john.johnson at gatech.edu><mailto:
> john.johnson at gatech.edu>
> he/him/his
>
> On 2 Mar 2020, at 16:43, Beach, Paul Anthony wrote:
>
> EEGLAB gurus,
>
> I’m working on creation of a STUDY between a control and patient group.
> During 'pre-compute channel measures’, selecting pre-computation of ERPs,
> power spectrum, and ERP-image I’m getting the following error:
>
> “Datasets to be concatenated do not have the same number of channels
> (Error occurred in function Eeg_getdatact(ct) at line 111)”
>
> It does this about half-way through the subject list (see output in Matlab
> below)
>
> Using Matlab v 2019a, eeglab-develop.
>
> Thanks!
> Paul
> --
> Paul Beach DO, PhD
> PGY4, Chief Resident Physician
> Department of Neurology
> Emory University School of Medicine
>
>
> (Matlab output prior to popup error)
> Channel merging warning: dissimilar fields in the two structures
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/PD/YES_DBS/PD08/08.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl11/11.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl12/12.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl13/13.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl14/14.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl15/15.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 2 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl16/16.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl17/17.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl18/18.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl19/19.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Interpolating 2 channels...
> Channel merging warning: dissimilar fields in the two structures
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/PD/YES_DBS/PD08/08.daterp'
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl11/11.daterp'
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl12/12.daterp'
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl13/13.daterp'
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl14/14.daterp'
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl15/15.daterp'
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl16/16.daterp'
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl17/17.daterp'
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl18/18.daterp'
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl19/19.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/PD/YES_DBS/PD08/08.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl11/11.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl12/12.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl13/13.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl14/14.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl15/15.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 2 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl16/16.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl17/17.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl18/18.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Removing baseline...
> Saving ERP file '/Volumes/Research_Beach/DATAS/EEG/PROCESSED
> EEG/Controls/Ctrl19/19.daterp'
> Channel merging warning: dissimilar fields in the two structures
> Interpolating 10 channels...
> Interpolating 2 channels...
>
>
>
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>
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