ind = D.pickconditions('conditionlabel');
should give you indices of trials for a particular condition that have
not been rejected
ind = setdiff(D.meegchannels, D.badchannels);
should give you indices of channels that have not been rejected
You can also use Other/'Remove bad trials' to physically remove the
rejected trials from the dataset.
Best,
Vladimir
On Fri, Nov 12, 2010 at 4:49 PM, Martin Jensen Dietz <[log in to unmask]> wrote:
> Hi Vladimir,
>
> I thought loading the artefact-rejected object would index only good channels and trials even though the data set has not been altered. Is there a sensible way of indexing good/bad trials that is available from the command line ?
>
> Best,
> Martin
>
>
> On Nov 12, 2010, at 5:31 PM, Vladimir Litvak wrote:
>
>> What code did you use to plot? Note that the artefact rejection
>> function does not remove trials from the dataset it just marks them as
>> bad. The same goes for channels. So if you haven't made sure that you
>> are plotting data that hasn't been rejected that might explain what
>> you are seeing.
>>
>> Vladimir
>>
>> On Fri, Nov 12, 2010 at 4:28 PM, Martin Jensen Dietz <[log in to unmask]> wrote:
>>> Hi Vladimir,
>>>
>>> For 32 channels that have been highpass filtered, lowpass filtered, epoched and artefact rejected with the following parameters
>>>
>>> S = [];
>>> S.D = fullfile(pth, D.fname);
>>> S.badchanthresh = 0.2;
>>> S.methods.channels = {'all'};
>>> S.methods.fun = 'threshchan';
>>> S.methods.settings.threshold = 80; % threshold in microvolts
>>> D = spm_eeg_artefact(S);
>>>
>>> the data still contain trials exceeding the threshold (shown for one channel with 1497 epochs). I get the same results when using the GUI.
>>>
>>> Best,
>>> Martin
>>>
>>> [cid:6159DA1C-1E40-45B7-BD9C-9C055E2750FE@akh06.auh.dk]
>>> On Nov 12, 2010, at 3:35 PM, Vladimir Litvak wrote:
>>>
>>> In principle it should work. Could it be that this channel was not
>>> among the ones that were examined or that it was marked as bad? You
>>> can put a breakpoint in spm_eeg_artefact_threshchan line 65 and see
>>> what's happening there. If you can't figure it out, send me an
>>> example.
>>>
>>> Vladimir
>>>
>>> On Fri, Nov 12, 2010 at 2:25 PM, Martin Jensen Dietz <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>>> Dear Vladimir & meeg'ers,
>>>
>>> When using microvolt thresholding for artefact rejection I would assume trials exceeding the specified threshold to be rejected. In this case, that does not seem to be the case for all trials (threshold was set to 70 microvolts). Am I missing something ?
>>>
>>>
>>>
>
>
