[Eeglablist] std_envtopo (plotchans and pvaf)

Thu May 9 10:56:32 PDT 2013

Dear Scott,

Yes I've seen it, and also seen negative variance too. These things
themselves do not mean evidence of a bug. However, I thought one cluster
showing pvaf of -505% is pathological and needs to be investigated.

Makoto

2013/5/9 Scott Makeig <smakeig at gmail.com>

> Makoto -   Cluster envelopes can indeed exceed the scalp ERP bounds -- IF
> the clusters contribute activity with different polarities at maximal
> projection channels.... whose sum is therefore smaller than the strongest
> cluster contribution, not larger...
>
> Scott
>
>
> On Wed, Apr 17, 2013 at 6:09 PM, Makoto Miyakoshi <mmiyakoshi at ucsd.edu>wrote:
>
>> Dear Ana,
>>
>> Sorry for slow response.
>>
>> Thanks Makoto. This is very helpful. I'd still love to be able to choose
>>> some channels though; My P300 comes along with an effect of an opposite
>>> (negative) signal in the frontal electrodes (I think this happens because I
>>> use the average as a reference), and I believe that choosing just some
>>> centro-parietal electrodes would give me a better estimate. I'll see if I
>>> can try something myself.
>>>
>>
>> Maybe you want to try my toolbox to backproject cluster ERPs to channels.
>> I'll send it to you in the separate mail.
>>
>> It seems to me that the line is pointing at 559 and what I'm talking
>>> about says "pvaf: 550.46. I had limited the latency anyway (from 200 to
>>> 600ms). Another example is the cluster close to it, which shows "pvaf:
>>> -111.61". This one is also pointing at latency ~559ms. I've attached an
>>> example of the output I get from std_envtopo.
>>>
>>
>> I saw it. It is quite strange indeed. I want to diagnose the situation.
>> At least I can tell that your 'outermost envelope' (shown in thick black)
>> is surpassed by other envelopes, which is not normal. That is like saying
>> some of your clusters have larger values than the sum of all (it's not
>> exactly like this but pretty much about it). Can you think of any reason
>> why you see this?
>>
>> If you can't find anything wrong by yourself, I need to ask you to either
>> 1. transfer all of your data to our server or 2. video conference by
>> sharing your desktop. You can choose whichever you want. Sorry for
>> inconvenience.
>>
>> Makoto
>>
>>
>> 2013/4/10 Ana Navarro Cebrian <anavarrocebrian at gmail.com>
>>
>>> >Currently this is not supported. I see how to do it though.
>>> I would suggest that you exclude clusters of non-interest, or specify
>>> the clusters to use, so that your outermost envelope is consist of only
>>> necessary ones.
>>>
>>> Thanks Makoto. This is very helpful. I'd still love to be able to choose
>>> some channels though; My P300 comes along with an effect of an opposite
>>> (negative) signal in the frontal electrodes (I think this happens because I
>>> use the average as a reference), and I believe that choosing just some
>>> centro-parietal electrodes would give me a better estimate. I'll see if I
>>> can try something myself.
>>>
>>> >-550.46 should be a number of latency. Where does the line (extending
>>> from the scalp topos) pointing? Isn't it -550.46 ms? If so, you should
>>> limit the latency window to evaluate contribution.
>>>
>>> It seems to me that the line is pointing at 559 and what I'm talking
>>> about says "pvaf: 550.46. I had limited the latency anyway (from 200 to
>>> 600ms). Another example is the cluster close to it, which shows "pvaf:
>>> -111.61". This one is also pointing at latency ~559ms. I've attached an
>>> example of the output I get from std_envtopo.
>>>
>>> >No, actually pvaf never sums to 100% if you add up each clusters. That
>>> means, pvaf(Cls1+Cls2) ~= pvaf(Cls1)+pvaf(Cls2). By the way the default
>>> 100% is pvaf(Cls1+Cls2+...ClsN) if you have N number of clusters.
>>> The measure pvaf is always superadditive i.e. exceeds 100% if summed
>>> separately.
>>>
>>> Here I was talking about the individual pvaf (for each individual
>>> cluster) shown under the cluster topoplot, and not the total pvaf. I'm not
>>> sure if the response is still the same.
>>> For example, for those two clusters that I'm talking about above, with
>>> pvaf -550.46% and -111.61%. Would it be possible to get positive values
>>> like those for individual clusters? i.e. pvaf: 550.46?
>>>
>>> Thank you again for your help, Makoto.
>>>
>>>
>>>
>>>
>>> 2013/4/10 Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
>>>
>>>> Dear Ana,
>>>>
>>>> >First, I was wondering wether I could use something like the
>>>> 'plotchans' (available in envtopo) to compute the contributions in just one
>>>> or a few channels of interest. The default function computes the
>>>> contributions for the grand ERPs which gives me a lot of variability that
>>>> I'm not interested in.
>>>>
>>>> Currently this is not supported. I see how to do it though.
>>>> I would suggest that you exclude clusters of non-interest, or specify
>>>> the clusters to use, so that your outermost envelope is consist of only
>>>> necessary ones.
>>>>
>>>> >Also, I'm still confuse about the pvaf for the individual clusters.
>>>> For example, I'm looking for the clusters that explain the P300
>>>> variability and there is a cluster (out of 7 clusters) that seems to me
>>>> (based on the cluster's ERP) that explains most of the variability of the
>>>> P300.
>>>> When I run std_envtopo, I get a pvaf of -550.46 for that cluster.
>>>> First, I understand that this is not talking about the P300 activity alone,
>>>> but the grand average, and this implicates a lot of variance from many
>>>> areas that I'm not interested in (and this is the reason why I'm trying to
>>>> use just a few channels of interest). Therefore, because what I think is
>>>> the 'P300 cluster' may have a different signal than all the other
>>>> activities (that I'm not interested in), then I get a negative value for
>>>> this cluster pvaf (-550.46). Am I getting something wrong so far?
>>>>
>>>> -550.46 should be a number of latency. Where does the line (extending
>>>> from the scalp topos) pointing? Isn't it -550.46 ms? If so, you should
>>>> limit the latency window to evaluate contribution.
>>>>
>>>> >Also, I imagine that, because this is the percent variance accounted
>>>> for, for positive numbers, 100 should be the maximum possible value?
>>>>
>>>> No, actually pvaf never sums to 100% if you add up each clusters. That
>>>> means, pvaf(Cls1+Cls2) ~= pvaf(Cls1)+pvaf(Cls2). By the way the default
>>>> 100% is pvaf(Cls1+Cls2+...ClsN) if you have N number of clusters.
>>>>
>>>> The measure pvaf is always superadditive i.e. exceeds 100% if summed
>>>> separately.
>>>>
>>>> Makoto
>>>>
>>>>  2013/4/10 Ana Navarro Cebrian <anavarrocebrian at gmail.com>
>>>>
>>>>> Hi,
>>>>>  I have two questions about the function std_envtopo.m
>>>>>
>>>>> First, I was wondering wether I could use something like the
>>>>> 'plotchans' (available in envtopo) to compute the contributions in just one
>>>>> or a few channels of interest. The default function computes the
>>>>> contributions for the grand ERPs which gives me a lot of variability that
>>>>> I'm not interested in.
>>>>>
>>>>> Also, I'm still confuse about the pvaf for the individual clusters.
>>>>> For example, I'm looking for the clusters that explain the P300
>>>>> variability and there is a cluster (out of 7 clusters) that seems to me
>>>>> (based on the cluster's ERP) that explains most of the variability of the
>>>>> P300.
>>>>> When I run std_envtopo, I get a pvaf of -550.46 for that cluster.
>>>>> First, I understand that this is not talking about the P300 activity alone,
>>>>> but the grand average, and this implicates a lot of variance from many
>>>>> areas that I'm not interested in (and this is the reason why I'm trying to
>>>>> use just a few channels of interest). Therefore, because what I think is
>>>>> the 'P300 cluster' may have a different signal than all the other
>>>>> activities (that I'm not interested in), then I get a negative value for
>>>>> this cluster pvaf (-550.46). Am I getting something wrong so far?
>>>>>
>>>>> Also, I imagine that, because this is the percent variance accounted
>>>>> for, for positive numbers, 100 should be the maximum possible value?
>>>>>
>>>>> I hope that makes sense. Thanks in advance for your help.
>>>>>  Ana
>>>>>
>>>>> _______________________________________________
>>>>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
>>>>> To unsubscribe, send an empty email to
>>>>> eeglablist-unsubscribe at sccn.ucsd.edu
>>>>> For digest mode, send an email with the subject "set digest mime" to
>>>>> eeglablist-request at sccn.ucsd.edu
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Makoto Miyakoshi
>>>> Swartz Center for Computational Neuroscience
>>>> Institute for Neural Computation, University of California San Diego
>>>>
>>>
>>>
>>>
>>> --
>>> Ana Navarro-Cebrian
>>> Postdoctoral Fellow. UCSF
>>>
>>
>>
>>
>> --
>> Makoto Miyakoshi
>> Swartz Center for Computational Neuroscience
>> Institute for Neural Computation, University of California San Diego
>>
>> _______________________________________________
>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
>> To unsubscribe, send an empty email to
>> eeglablist-unsubscribe at sccn.ucsd.edu
>> For digest mode, send an email with the subject "set digest mime" to
>> eeglablist-request at sccn.ucsd.edu
>>
>
>
>
> --
> Scott Makeig, Research Scientist and Director, Swartz Center for
> Computational Neuroscience, Institute for Neural Computation, University of
> California San Diego, La Jolla CA 92093-0559, http://sccn.ucsd.edu/~scott
>

-- 
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://sccn.ucsd.edu/pipermail/eeglablist/attachments/20130509/9af18077/attachment.html>