clusterrandomization

[Olga Sysoeva]

Please disregard my previous post. Now I know how to do this. Sorry...

----- Original Message -----
From: "Olga Sysoeva" <olga at GRAPHICMIND.INFO>
To: <FIELDTRIP at NIC.SURFNET.NL>
Sent: Thursday, May 11, 2006 9:02 PM
Subject: Re: [FIELDTRIP] clusterrandomization


> OK. I think my negcluster is not close to significance (p=0.5), therefore
> I do not want to plot it.
> How can I choose to plot Only significant clusters (I have 3 posclusters
> only 1 of which is significant)?
> I guess I need to change something in mask option, but I do not know how
> to use the squeeze option. Can you help me with this?
>
> Best Regards,
> Olga
>
> ----- Original Message -----
> From: "Vladimir Litvak" <litvak at TECHUNIX.TECHNION.AC.IL>
> To: <FIELDTRIP at NIC.SURFNET.NL>
> Sent: Thursday, May 11, 2006 9:52 PM
> Subject: Re: [FIELDTRIP] clusterrandomization
>
>
> Sometimes you want to know what's happening in your data. The significance
> threshold is arbitrary and also there are parameters that can be modified
> to
> make the procedure more sensitive to particular kinds of effects (though
> one
> should not get carried away with that). So it can be useful to know that
> there is an effect close to significance somewhere or conversely all the
> clusters are small.
>
> Vladimir
>
> -----Original Message-----
> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> Behalf
> Of Olga Sysoeva
> Sent: Thursday, May 11, 2006 6:48 PM
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] clusterrandomization
>
> But why than to plot them if they are not significant?
>
> ----- Original Message -----
> From: "Vladimir Litvak" <litvak at TECHUNIX.TECHNION.AC.IL>
> To: <FIELDTRIP at NIC.SURFNET.NL>
> Sent: Thursday, May 11, 2006 9:38 PM
> Subject: Re: [FIELDTRIP] clusterrandomization
>
>
> clusrand.posclusters and clusrand.negclusters contain all the clusters
> found, not just the significant ones.
>
> Vladimir
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> Behalf
> Of Olga Sysoeva
> Sent: Thursday, May 11, 2006 6:30 PM
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: [FIELDTRIP] clusterrandomization
>
> Thank you very much for the help.
>
> I continue my succes with Clasterrandomization analysis on within-subject
> disign.
> I applied clasterrandomization to compare two condition. I mostly use the
> settings
> from the tutorial (both cfg.alphathres =0.05 and cfg.alpha=0.05) and got
> positive and negative clusters
> (both clusrand.posclusters and clusrand.negclusters not empty). But when I
> look for the pval for neg cluster
> (which is only one, size 8) it appeared to be 0.51. It is bigger than our
> threshold (0.05). Why it is mark as
> significant cluster than (clusrand.negclusterlabelmat =1 for 8 elements)?
> Could somebody comment on it?
>
> Best Regards,
> Olga.
>
> ----- Original Message -----
> From: "Robert Oostenveld" <r.oostenveld at FCDONDERS.RU.NL>
> To: <FIELDTRIP at NIC.SURFNET.NL>
> Sent: Monday, May 08, 2006 11:16 AM
> Subject: Re: [FIELDTRIP] first success!!!
>
>
>>> I want to share my first success in using Filedtrip. Although I  could
>>> still not properly load my current 64 electrodes data, I  succeeded in
>>> importing my old 19 channel data. Moreover, I succeded  in conducting
>>> the
>
>>> between-trial clasterrandomization analysis!
>>
>> It might be that the automatic projection of the 3D electrodes to the  2D
>> surface for plotting is not optimal for your 64 channel set,  perhaps due
>> to a few very low electrodes. I suggest that you  construct a layout
>> file,
>
>> see my previous mail. You can also look into  the code in
>> private/createlayout, where at the bottom you will find  some code that
>> helps you to  visualise the layout.
>>
>>> But I still have problems with within-subject cluster- randomization.
>>> The
>
>>> error "did not find the gradiometer or electrode  information" appears,
>>> line 461. What could it be?
>>
>> Cluster randomization requires that the neighbourhood geomerty in the
>> data is known, i.e. the neighbouring electrodes. You can specify them
>> with cfg.neighbours. It is documented in "help clusterrandanalysis".  One
>> method to automatically specify the neighbourhood is by having  electrode
>> information in the dataset, i.e. an elec structure and to  specify the
>> cfg.neighbourdist option (default is 4 cm, which is  suitable for the CTF
>> gradiometers). I do not know the units of your  electrodes (could be m,
>> cm, mm, or unit-scaled dimensionless), but  the cfg.neighbourdist should
>> be specified in the same units.
>>
>> best regards,
>> Robert