[Eeglablist] Problems with epoch rejection

[Makoto Miyakoshi]

Dear Ana,

> based on Makoto's pipeline

You will receive an invoice from me.

> 0/1 trial(s) marked for rejection

The first guess I had was whether this is by any chance continuous data.

Makoto



On Tue, Jan 21, 2020 at 11:46 AM ANA BUJAN <ana.bujan at gmail.com> wrote:

>   Dear all,
>
> I have been trying to reject raw epochs (no ICA) through a handmade script
> based on Makoto's pipeline with some changes. I would like to perform
> rejection of epochs by all methods of rejection as the last pre-processing
> step. However, each way I have tried, I got an error. I'm not a proficient
> person programming and relatively new with EEGlab. So, it is almost for
> sure I'm doing something wrong but I'm not able to see it...
> So, I will make clear my point in order for you to be able to figure out
> what I'm doing wrong. These the steps of the script:
>
> 1. Import Biosig data.
> 2. Set channel locs
> 3. Remove baseline and filters (0.5-40)
> 4. Bad channels rejection through pop_rejchan
> 5. Remove bad data segments with ASR
> 6. ICA and IC label for correction of artifacts (by the way, sometimes, no
> always, EEG = pop_iclabel in the script doesn't work, the error is :
>
> Undefined function or variable 'pop_iclabel'.
> Error in rs_batchcode_superpose (line 45)
>     EEG = pop_iclabel(EEG, 'default')
> 7. Interpolation of removed channels and average reference
> 8. Epochs extraction
> 9. Epochs rejection
>
> So, this last step is where I'm having trouble. I've tried three options:
>
> OPTION 1. Mark the bad epochs, then superpose, then reject
>
>     EEG = pop_eegthresh(EEG,1,[1:64] ,-100,100,0,1.998,2,0);
>     EEG = pop_rejtrend(EEG,1,[1:64] ,1024,75,0.3,2,0);
>     EEG = pop_jointprob(EEG,1,[1:64] ,5,5,0,0,0,[],0);
>     EEG = pop_rejkurt(EEG,1,[1:64] ,5,5,0,0,0,[],0);
>     EEG = pop_rejspec( EEG, 1,'elecrange',[1:64]
> ,'method','multitaper','threshold',[-50 50;-100 25],'freqlimits',[0 2;20
> 40],0,0);
>     EEG = eeg_rejsuperpose( EEG, 1, 1, 1, 1, 1, 1, 1, 1);
>     EEG = pop_rejepoch( EEG, [EEG.reject.rejglobal] ,0);
>
> This way the code got staked at pop_rejspec, so it never finishes, and I
> don' understand why.... I copied the code from the history file....
>
> When I try this same option but erasing the rejection for spectra, I got
> his error:
>
> *******************************************************************************************
> 64 channel selected
> 0/86 trials marked for rejection
> Selecting trials...
> 64 channel(s) selected
> 0/86 trial(s) marked for rejection
> The following trials have been marked for rejection
>
> Computing joint probability for channels...
> Computing all-channel probability...
> 3/86 trials marked for rejection
> 3 trials marked for rejection
> Computing kurtosis for channels...
> Computing all-channel kurtosis...
> 6/86 trials marked for rejection
> 6 trials marked for rejection
> Error using  |
> Matrix dimensions must agree.
>
> Error in eeg_rejsuperpose>rejarray (line 135)
> dest = dest | ori;
>
> Error in eeg_rejsuperpose (line 81)
> rejglobalE = rejarray( rejglobalE, EEG.reject.rejconstE);
>
> Error in rs_batchcode_superpose (line 105)
>     EEG = eeg_rejsuperpose( EEG, 1, 1, 1, 1, 1, 1, 1, 1);
>
> >>
>
>
> ****************************************************************************************
>
> OPTION 2: Marked bad epochs (without pop_rejspec, because there is no
> variable for this in the EEG > reject), reject the marked ones
>
>     EEG = pop_eegthresh(EEG,1,[1:64] ,-100,100,0,1.998,0,0);
>     EEG = pop_rejtrend(EEG,1,[1:64],1024,75,0.3,0,0);
>     EEG = pop_jointprob(EEG,1,[1:64],5,5,0,0,0,[],0);
>     EEG = pop_rejkurt(EEG,1,[1:64],5,5,0,0,0,[],0);
>
>     EEG = pop_rejepoch( EEG,[EEG.reject.rejthresh, EEG.reject.rejkurt,
> EEG.reject.rejconst, EEG.reject.rejfreq],0);
>
> In this case, the epochs are marked, but when the first rejection is
> performed (by threshold), the epochs info is not longer then, and the set
> has just 1 epoch... Of course, after this, the rest of the rejections is
> not performed...
>
> *******************************************************************************************
> 64 channel selected
> 11/89 trials marked for rejection
> Selecting trials...
> 64 channel(s) selected
> 1/89 trial(s) marked for rejection
> The following trials have been marked for rejection
> 1
> Computing joint probability for channels...
> Computing all-channel probability...
> 2/89 trials marked for rejection
> 2 trials marked for rejection
> Computing kurtosis for channels...
> Computing all-channel kurtosis...
> 8/89 trials marked for rejection
> 8 trials marked for rejection
> 20/89 trials rejected
> Removing 11 trial(s)...
> Pop_select: removing 22 unreferenced events
> eeg_checkset note: data array made 3-D
> eeg_checkset warning: 3rd dimension size of data (1) does not match the
> number of epochs (78), corrected
> eeg_checkset note: upper time limit (xmax) adjusted so (xmax-xmin)*srate+1
> = number of frames
>
> *********************************************************************************************************************************
> OPTION 3: Reject the epochs directly instead of marking them.
>
>     EEG = pop_eegthresh(EEG,1,[1:64],-100,100,0,1.998,0,1);
>     EEG = pop_rejtrend(EEG,1,[1:64],1024,75,0.3,0,1);
>     EEG = pop_jointprob(EEG,1,[1:64] ,5,5,0,1,0,[],0);
>     EEG = pop_rejkurt(EEG,1,[1:64] ,5,5,0,1,0,[],0);
>     EEG = pop_rejspec( EEG, 1,'elecrange',[1:64]
> ,'method','multitaper','threshold',[-50 50;-100 100],'freqlimits',[0 2;20
> 40],'eegplotcom','','eegplotplotallrej',0,'eegplotreject',1);
>
> It happens the same as in the previous option: after the first rejection id
> made, there are no longer epochs. This is the error:
>
> **********************************************************************************************************************************
> 64 channel(s) selected
> 0/1 trial(s) marked for rejection
> The following trials have been marked for rejection
>
> 0/1 trials rejected
> Computing joint probability for channels...
> Computing all-channel probability...
> 0/1 trials marked for rejection
> 0 trials marked for rejection
> 0/1 trials rejected
> Computing kurtosis for channels...
> Computing all-channel kurtosis...
> 1/1 trials marked for rejection
> 1 trials marked for rejection
> 1/1 trials rejected
> Error using pop_select (line 227)
> Error: dataset is empty
>
> Error in pop_rejepoch (line 96)
> EEG = pop_select( EEG, 'notrial', tmprej);
>
> Error in pop_rejkurt (line 269)
>         EEG = pop_rejepoch(EEG, rej, 0);
>
> Error in proof_rejall (line 104)
>     EEG = pop_rejkurt(EEG,1,[1:64] ,5,5,0,1,0,[],0);
>
> **********************************************************************************************************
> I apologize for the long message, but I wanted to make clear all the things
> I checked. So, this is all, let me know if you need more info or files to
> replicate the errors or whatever.
>
> Many thanks for a great job.
>
> Ana Buján
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