[Eeglablist] comparing condition and group ERP's from a STUDY
Eduardo Vianna
eduardo.vianna at ucla.edu
Wed Oct 22 19:01:03 PDT 2008
Dear Hamish,
I have been running into the same problem as yours. I also noticed that the
number of subjects you have in each group is different (this was also my
case). I have run a test with same number of subjects in both groups (for
tutorial data and my own data), and plotting ERP data works. However, when
a run my data with different number of subjects in each group, I get the
same problem you described. Plotting ERSP and ITC should work fine with
different number of subjects per group, but plotting ERP and Spectra results
don¹t.
Eduardo Vianna, PhD
Center for Neurobiology of Stress
Division of Digestive Diseases
University of California, Los Angeles
10945 Le Conte Ave., Ste 2338C
Los Angeles, CA 90095
On 10/19/08 6:06 PM, "Hamish INNES-BROWN" <HINNES-BROWN at bionicear.org>
wrote:
> Hi Arno, thanks for your reply.
>
> The weird thing is, I'm certain that all your points below are true. Both
> conditions are present in all subjects, and the group really is a group (ie
> groups '1' and '2' have different subjects - children vs adults, and are not
> ways to sneak in extra conditions).
>
> Just to be sure, I wrote a short script to save the EEG.setnames, EEG.group,
> EEG.condition, EEG.ntrials, pnts, srate, xmin and xmax for all the sets in the
> Study to a csv file, and all was correct.
>
> % script for extracting the number of trials of each stimulus, for each
> % subject in a STUDY.
> %STUDY must be currently open
> % loop over sets in study.
>
> nsets = size(STUDY.datasetinfo,2)
>
> %make an empty matrix to fill up with the data
> %rows = sets
> output = zeros(nsets, 8);
>
> for currentset = 1:nsets;
> csetname = EEG(currentset).setname;
> ID = str2num(csetname(2:4));
> output(currentset,1) = ID;
> output(currentset,2) = str2num(EEG(currentset).group) ;
> output(currentset,3) = str2num(EEG(currentset).condition);
> output(currentset,4) = EEG(currentset).trials ;
> output(currentset,5) = EEG(currentset).pnts ;
> output(currentset,6) = EEG(currentset).srate ;
> output(currentset,7) = EEG(currentset).xmin ;
> output(currentset,8) = EEG(currentset).xmax ;
> end
>
> Results here if interested
> http://spreadsheets.google.com/ccc?key=pMWrciDbEoFRAgnrYtXy9MQ
> <http://spreadsheets.google.com/ccc?key=pMWrciDbEoFRAgnrYtXy9MQ&inv=hinnesbrow
> n at gmail.com&t=4926724069117154563&guest>
>
> The other weird thing is that every other plotting button works perfectly
> well, I can see Spect, ERSP, and ITC plots for both conditions and groups,
> which makes me think the data must be OK, as I guess all these measures are
> being calculated from the same data..?
>
>
> And all the electrodes are interpolated - I ended up using v6.01 just to do
> the electrode interpolation, then switching back to 6.03b(oct2008) to pre-calc
> all the channel measures. Selecting the individual setfiles and plotting
> ERP's also works fine, for both groups and condition types, so I dont think
> the data is missing or wrongly arranged. Any other hints?
>
> Many thanks!
>
>
> Hamish Innes-Brown
> Senior Research Officer
>
> The Bionic Ear Institute
> Auditory Clinical Neuroscience Unit
> c/o St Vincents Hospital
> 6th Floor Daly Wing,
> 35 Victoria Pde, Fitzroy Vic 3065
> Tel: +61 3 9288 3523
> Fax: +61 3 6997 7518
>
>
>
>
> From: eeglablist-bounces at sccn.ucsd.edu
> [mailto:eeglablist-bounces at sccn.ucsd.edu] On Behalf Of arno delorme
> Sent: Saturday, 18 October 2008 9:58 PM
> To: Hamish INNES-BROWN
> Cc: eeglablist at sccn.ucsd.edu
> Subject: Re: [Eeglablist] comparing condition and group ERP's from a STUDY
>
> Dear Hamish,
>
> some more information about groups and conditions. Optimally:
>
> - All conditions are supposed to be present in all subjects. If not, the
> program should still work but might lead to the empty plots you are seeing
> them right now.
> - Groups are supposed to be for different subjects or different sessions
> (different ICA decomposition for sure). Using groups within the same subjects
> (to define a second condition) might work but not always. This is pushing the
> limits of the program.
> - You should interpolate missing electrodes. Once more, if you do not do that,
> the program should work but the average will take into account different
> subjects at each channel location.
>
> We are working on these limitations. You will be able to select several
> conditions and/or groups.
>
> Best,
>
> Arno
>
> On 14 oct. 08, at 07:35, Hamish INNES-BROWN wrote:
>
>>
>>
>>
>> Hi EEGLAB list.
>>
>>
>> I'm currently trying to track down the source of a problem i have plotting
>> condition and group ERP's from the STUDY channel measures menu.
>>
>>
>> I have all the 'group' and 'condition' data loaded into the EEG.group and
>> EEG.condition. The correct group and condition numbers pop up in the study
>> info window when all the subjects are loaded into the study.. In EEG.group
>> and EEG.condition the values are strings (but numerals). I have groups '1'
>> and '2', and conditions '111' and '122'.
>>
>>
>> The study looks like this
>>>> >> STUDY
>> STUDY =
>> name: 'Study1'
>> datasetinfo: [1x58 struct]
>> cluster: [1x1 struct]
>> changrp: [1x63 struct]
>> task: ''
>> notes: ''
>> filename: 'STUDY_ALL.study'
>> filepath: 'D:\_PROJECTS\_FB\_ANALYSIS\__EEGLAB\SET\08STUDY_ALL\'
>> history: [1x3126 char]
>> subject: {1x29 cell}
>> group: {'1' '2'}
>> session: []
>> condition: {'111' '122'}
>> setind: [2x29 double]
>> etc: [1x1 struct]
>> preclust: [1x1 struct]
>> saved: 'yes'
>>
>>
>> Now, when plotting the channel measures, I select "plot conditions on the
>> same panel", and get two plots as expected. The first (group '1') has two
>> lines, as expected. One is labelled '111' and the other '122'. All OK.
>> However underneath there is an empty plot, labelled '2', but with no lines.
>>
>>
>> I thought this might be somehow a fault in my data or the way the conditions
>> and groups are entered (maybe they should be numbers, not strings?) so I
>> tried loading the example data (5subjects.zip), and added a group variable.
>> Same problem however.
>>
>>
>>
>> Anyone had any luck with this before?
>>
>>
>> Many thanks
>>
>>
>>
>>
>>
>> Hamish Innes-Brown
>> Senior Research Officer
>>
>>
>> The Bionic Ear Institute
>> Auditory Clinical Neuroscience Unit
>> c/o St Vincents Hospital
>> 6th Floor Daly Wing,
>> 35 Victoria Pde, Fitzroy Vic 3065
>> Tel: +61 3 9288 3523
>> Fax: +61 3 6997 7518
>> _______________________________________________
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