[FieldTrip] What exactly does 'minnbchan' refer just to spatial neighbors?

Thu Feb 10 12:33:05 CET 2011

Hi Eric,

sorry that I called this a "side-effect", I indeed find it most practical myself. I just didn't know this was the intended purpose.

Michael

-----Ursprüngliche Nachricht-----
Von: "Eric Maris" <e.maris at donders.ru.nl>
Gesendet: Feb 10, 2011 11:16:05 AM
An: "'Email discussion list for the FieldTrip project'" <fieldtrip at donders.ru.nl>
Betreff: Re: [FieldTrip] What exactly does 'minnbchan' refer just to spatial neighbors?

>Hi Michael,
>
>> there is one additional side effect of specifying a LARGE minnbchan
>> that actually leads to SMALLEr clusters in a certain sense. If I
>> understand correctly, at any point in time&frequency the cluster has to
>> have a spatial extension of minnbchan+1. So when you specify a large
>> value the cluster may more easily be cut up into several smaller ones
>> along the space&time dimension - which may or may not  be desirable.
>
>Whether it is a side effect or not, depends on how you look at it. For me it is its intended effect. I implemented the minnbchan-parameter after discussions with PhD-students that applied the cluster-based permutation statistics on channel-time-frequency data and produced significant clusters with weird shapes. Often, these shapes contained narrow "bridges" connecting nearby blobs in channel-time-frequency space. By increasing minnbchan, these bridges were removed and only the blobs remained.
>
>Although I understand the requests of the PhD-students that I discussed with, I find the discussions about the minnbchan-parameter not very rewarding. In fact, it is looking for isolated blobs that one would like to interpret as separate physiological entities. This contrast with the nature of the EEG/MEG data, which has poor spatial resolution (due to volume conduction and common pick-up), often poor spectral resolution (due to the short time windows of our time-resolved spectral analysis), and often poor time resolution (due to latency jitter over trials).
>
>Best,
>
>Eric
>
>
>
>
>
>> 
>> Michael
>> 
>> -----Ursprüngliche Nachricht-----
>> Von: "David Groppe" <dgroppe at cogsci.ucsd.edu>
>> Gesendet: Feb 8, 2011 7:18:59 PM
>> An: "Email discussion list for the FieldTrip project"
>> <fieldtrip at donders.ru.nl>
>> Betreff: Re: [FieldTrip] What exactly does 'minnbchan' refer just to
>> spatial neighbors?
>> 
>> >On Tue, Feb 8, 2011 at 11:01 AM, Eric Maris <e.maris at donders.ru.nl>
>> wrote:
>> >> Dear David,
>> >>
>> >>
>> >>> Thanks very much for the email Eric, but I'm confused as to why you
>> >>> answered "No" to my second comment.  From what I understand, if you
>> >>> use a value of minnbchan that is greater than 0, then any
>> >>> significant clusters will necessarily spread across multiple
>> >>> electrodes.  For example, if you set minnbchan to 1, then all
>> >>> significant clusters will have to include at least two electrodes
>> so
>> >>> that each significant "voxel" has at least one neighbor at another
>> >>> electrode.  Thus, if your effect is truly at only a single
>> >>> electrode, having a value of minnbchan greater than 0 will force
>> you
>> >>> to miss the effect or to think it occurs at more electrodes than it
>> >>> really does.  What part of my reasoning is incorrect?
>> >>
>> >> Your reasoning is correct and mine was incorrect. I should read
>> >> better before I write. My apologies for this.
>> >
>> >Got it. Thanks very much for clarifying Eric.
>> >
>> >>
>> >> I do have to qualify that with minnbchan=0 it may also happen that
>> >> your significant cluster contains more than one electrode (the
>> >> electrode with the true effect plus some surrounding ones that by
>> >> accident exceed the threshold that is used to identify clusters).
>> >
>> >That makes perfect sense.  Since our lab uses only a limited number of
>> >electrodes (32), I wanted to make sure I understood the minimum number
>> >of electrodes an effect needs to span to be detected.
>> >      once again, I very much appreciate your answers to my questions,
>> >              -David
>> >
>> >> Best,
>> >>
>> >> Eric
>> >>
>> >>
>> >>
>> >>
>> >>>      again, thanks very much for the help,
>> >>>             -David
>> >>>
>> >>>
>> >>> > Best,
>> >>> >
>> >>> > Eric
>> >>> >
>> >>> >
>> >>> > dr. Eric Maris
>> >>> > Donders Institute for Brain, Cognition and Behavior Radboud
>> >>> > University P.O. Box 9104 6500 HE Nijmegen The Netherlands
>> >>> > T:+31 24 3612651
>> >>> > Mobile: 06 39584581
>> >>> > F:+31 24 3616066
>> >>> > mailto:e.maris at donders.ru.nl
>> >>> > http://www.nphyscog.com/
>> >>> >
>> >>> >
>> >>> >
>> >>> >
>> >>> >
>> >>> >
>> >>> >
>> >>> >
>> >>> >>     thanks for your help,
>> >>> >>         -David
>> >>> >>
>> >>> >>
>> >>> >> --
>> >>> >> David Groppe, Ph.D.
>> >>> >> dgroppe at cogsci.ucsd.edu
>> >>> >> http://www.cogsci.ucsd.edu/~dgroppe/
>> >>> >> _______________________________________________
>> >>> >> fieldtrip mailing list
>> >>> >> fieldtrip at donders.ru.nl
>> >>> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> >>> >
>> >>> > _______________________________________________
>> >>> > fieldtrip mailing list
>> >>> > fieldtrip at donders.ru.nl
>> >>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> >>> >
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> David Groppe, Ph.D.
>> >>> Postdoctoral Researcher
>> >>> Kutaslab
>> >>> Dept. of Cognitive Science
>> >>> University of California, San Diego
>> >>> http://www.cogsci.ucsd.edu/~dgroppe/
>> >>>
>> >>> _______________________________________________
>> >>> fieldtrip mailing list
>> >>> fieldtrip at donders.ru.nl
>> >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> >>
>> >>
>> >>
>> >> _______________________________________________
>> >> fieldtrip mailing list
>> >> fieldtrip at donders.ru.nl
>> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> >>
>> >
>> >
>> >
>> >--
>> >David Groppe, Ph.D.
>> >Postdoctoral Researcher
>> >Kutaslab
>> >Dept. of Cognitive Science
>> >University of California, San Diego
>> >http://www.cogsci.ucsd.edu/~dgroppe/
>> >
>> >_______________________________________________
>> >fieldtrip mailing list
>> >fieldtrip at donders.ru.nl
>> >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
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