[Eeglablist] re-reference with EGI data

Wed Aug 29 18:02:45 PDT 2012

>
> I've tended to import continuous files EGI RAW files into EEGLAB and to go
> from there. There may be few or no time points or epochs in one of the raw
> files. The message looks like it's just saying that it found no epochs and
> changed it to 1 big epoch for eeglab. Happy brain maps, stay in touch
> regarding your adventure.

On Wed, Aug 29, 2012 at 12:39 PM, Joshua Hartshorne
<jkhartshorne at gmail.com>wrote:

> Thanks, Stephen, Tarik, Simon,
>
> I am using the older GSN (pre-HydroCel) caps. EEGLab seems to correctly
> decide which locations file to use, and that file matches the one on EGI's
> website.
>
> I did notice, however, an odd warning when importing, which makes me
> worried and makes me wonder if any of you know something about it.
> Invariably, I get this message:
>
> eeg_checkset warning: 3rd dimension size of data (1) does not match the
> number of epochs (0), corrected
> eeg_checkset warning: number of columns in data (501045) does not match
> the number of points (0): corrected
>
> Here is all the output, just so you can see that warning in context:
>
>  Removing trailing character of selected file to find base file name
>
> Base file name is:
> /Users/jkh80/Documents/EEG_Data/ScalarImplicature/SI_Filtered_Raw/SI20
>
> Importing
> /Users/jkh80/Documents/EEG_Data/ScalarImplicature/SI_Filtered_Raw/SI20001.raw
>
> Importing binary EGI data file ...
>
> Importing
> /Users/jkh80/Documents/EEG_Data/ScalarImplicature/SI_Filtered_Raw/SI20002.raw
>
> Importing binary EGI data file ...
>
> Importing
> /Users/jkh80/Documents/EEG_Data/ScalarImplicature/SI_Filtered_Raw/SI20003.raw
>
> Importing binary EGI data file ...
>
> Importing
> /Users/jkh80/Documents/EEG_Data/ScalarImplicature/SI_Filtered_Raw/SI20004.raw
>
> Importing binary EGI data file ...
>
> Importing
> /Users/jkh80/Documents/EEG_Data/ScalarImplicature/SI_Filtered_Raw/SI20005.raw
>
> Importing binary EGI data file ...
>
> Importing
> /Users/jkh80/Documents/EEG_Data/ScalarImplicature/SI_Filtered_Raw/SI20006.raw
>
> Importing binary EGI data file ...
>
> Importing
> /Users/jkh80/Documents/EEG_Data/ScalarImplicature/SI_Filtered_Raw/SI20007.raw
>
> Importing binary EGI data file ...
>
> Importing
> /Users/jkh80/Documents/EEG_Data/ScalarImplicature/SI_Filtered_Raw/SI20008.raw
>
> Importing binary EGI data file ...
>
> Importing
> /Users/jkh80/Documents/EEG_Data/ScalarImplicature/SI_Filtered_Raw/SI20009.raw
>
> Importing binary EGI data file ...
>
> Importing
> /Users/jkh80/Documents/EEG_Data/ScalarImplicature/SI_Filtered_Raw/SI20010.raw
>
> Importing binary EGI data file ...
>
> Importing
> /Users/jkh80/Documents/EEG_Data/ScalarImplicature/SI_Filtered_Raw/SI20011.raw
>
> pop_chanevent: importing events from data channel 166 ...
>
> eeg_checkset warning: 3rd dimension size of data (1) does not match the
> number of epochs (0), corrected
>
> eeg_checkset warning: number of columns in data (991630) does not match
> the number of points (0): corrected
>
> eeg_checkset note: upper time limit (xmax) adjusted so (xmax-xmin)*srate+1
> = number of frames
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 165 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 164 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 163 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 162 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 161 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 160 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 159 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 158 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 157 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 156 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 155 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 154 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 153 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 152 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 151 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 150 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 149 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 148 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 147 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 146 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 145 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 144 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 143 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 142 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 141 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 140 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 139 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 138 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 137 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 136 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 135 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 134 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 133 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 132 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 131 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> pop_chanevent: importing events from data channel 130 ...
>
> eeg_checkset note: creating the original event table (EEG.urevent)
>
> Removing 1 channel(s)...
>
> Deleting empty data reference channel (reference channel location is
> retained)
>
> EGI channel location automatically detected GSN129.sfp ********* WARNING
> please check that this the proper file
>
>
>
> The data end up looking reasonable, so I'm not too worried about this, but
> I'd like to make sure it's not something I should worry about.
>
> Thanks,
>
> Josh
>
>
> On Wed, Aug 29, 2012 at 2:49 PM, Simon-Shlomo Poil <
> poil.simonshlomo at gmail.com> wrote:
>
>> Dear Joshua,
>>
>> This is known issue with the EGI electrode files. You simply need to
>> delete the additional channels.
>>
>> Try to use one of the two channel location files I have attached.
>> However, first carefully check that the layout is the same as your cap (EGI
>> has different layouts!).
>>
>> Hope it works,
>> Simon
>>
>> --
>> Simon-Shlomo Poil
>> http://www.nbtwiki.net
>>
>> 2012/8/24 Joshua Hartshorne <jkhartshorne at gmail.com>
>>
>>> I have EGI data recorded with a 128 electrode cap (vertex reference). I
>>> exported it to EEGLab and included the reference in the export (I used the
>>> multiple file format).
>>>
>>> EEGLab seems to recognize everything fine and includes 128 electrodes in
>>> the data, though when I go to "edit channel locations", I see 132 channels.
>>> The last one is my reference channel, labeled correctly as Cz. Though it's
>>> channel type is listed as "REF", no Reference is listed in the pop-up
>>> window (the section below the panel of "channel type") for any channel. I
>>> have no idea what channels 129-131 are (they are labeled FidNz, FidT9, and
>>> FidT10).
>>>
>>> So I want to re-reference. If I check "compute average reference", I
>>> don't have the option of retaining the old reference channel, which seems
>>> odd. If I click on the "..." button after "Add current reference channel
>>> back to the data", I get an error (??? Error using ==> waitfor Error while
>>> evaluating uicontrol Callback). From the wiki, I understand I should have
>>> gotten a list. Manually setting reference to "Cz" or "132" using the "edit
>>> channel info" window for channels 1:128 doesn't fix this problem.
>>>
>>> However, if I leave all that blank, I "successfully" re-reference to
>>> average reference. That is, I don't get an error, though I'm not sure how
>>> to determine whether it worked correctly or not.
>>>
>>> What I'd really like to do is re-reference to the average of the
>>> mastoids (channels 57 and 101), which would aid comparison with another
>>> dataset that was collected on different equipment with fewer electrodes.
>>> But the wiki suggests that I have to do this by going through average
>>> reference first (really?), so I wanted to make sure I had that much right
>>> first.
>>>
>>> In any case, I assume that if I list two electrodes in the "re-reference
>>> data to channel(s):" box that it will automatically compute the average of
>>> those two. I tried doing that (both with and without going through average
>>> reference), and I notice that channels 57 and 101 are *not* listed as "REF"
>>> in "Channel type" after doing this, while Cz is still listed as "REF",
>>> though "Reference" is now listed as "E57 E101".
>>>
>>> I appreciate any help.
>>> Josh Hartshorne
>>>
>>> _______________________________________________
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>>
>>
>>
>> --
>>
>>  <http://www.kispi.uzh.ch/Kinderspital/Medizin/mrzentrum_en.html>
>>
>
>
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