[FieldTrip] source statistics with ROI yields NaN clusters

[Roey]

Hi Vitoria and everyone else,

I agree with Jörn (thank you!) , indeed it seems this is the same problem. Hopefully I'll get back to it next week and maybe figure it out. Right now it seems like the A side consists of all the inside-voxels, whereas the B side consists of the different ROIs, and hence the mismatch.

A possible solution could be having the atlas we are using available to that function, and translating the B side to the voxel space.

By the way, are you using an MNI grid per subject?

Best,
roey



ב-16 באוק 2013, בשעה 17:07, "Jörn M. Horschig" <jm.horschig at donders.ru.nl> כתב/ה:

> Hi Vitoria,
> 
> I guess that is the same error that Roey Schurr described a few days back. There were some changes recently in the atlas lookup function (we replaced one function and made another more general). Apparently that broke some things, or you two just happen to do this as the first ever ;)
> The only thing I can think of is that you might need to interpolate to the MNI template so that the dimensions are matched between the atlas and your source structures. Could you give that a try and let us know whether that helps? 
> 
> Best,
> Jörn
> 
> 
> On 10/16/2013 11:19 AM, Vitória Magalhães Piai wrote:
>> Dear all, 
>> 
>> I'm trying to run ft_sourcestatistics with a specified ROI. It's data (MNEs) averaged over time.
>> 
>> If I run ft_sourcestatistics without an ROI, I get a cluster with prob = .178. It looks like this (figure attached), where I masked using the t-values.
>> Since I'm dealing with an N400-like component, I've got good reasons to expect the effect to be localised (mainly) to left temporal areas. 
>> 
>> So I tried adding this to my cfg:
>> 
>> cfgst.atlas        =  'aal\ROI_MNI_V4.nii';
>> cfgst.roi          = {'Temporal_Mid_L'  'Temporal_Sup_L'  'Temporal_Inf_L' };
>> cfgst.avgoverroi   = 'yes';
>> cfgst.hemisphere   = 'left';
>> cfgst.inputcoord   = 'mni' ;
>> stat = ft_sourcestatistics(cfgst, iRel{:}, iIde{:}); 
>> 
>> If cfgst.avgoverroi   == 'yes'; I get the following error:
>> 
>> ??? In an assignment  A(:) = B, the number of elements in A and B
>> must be the same.
>> Error in ==> clusterstat at 187
>>     tmp(cfg.inside) = postailobs;
>> Error in ==> ft_statistics_montecarlo at 326
>>   [stat, cfg] = clusterstat(cfg, statrand,       statobs,'issource',issource);
>> Error in ==> statistics_wrapper at 298
>>     [stat, cfg] = statmethod(cfg, dat, design, 'issource',issource);
>> Error in ==> ft_sourcestatistics at 107
>>     [stat, cfg] = statistics_wrapper(cfg, varargin{:});
>> 
>> If cfgst.avgoverroi   == 'no'; 
>> ft outputs "found  positive clusters in observed data" and stat.posclusters/negclusters is only NaN. This is regardless of whether cfgst.roi is one label or a cell array.
>> 
>> Does anyone know what I'm doing wrong?
>> I've been completely stuck on source statistics for these MNEs for days, so any help would be highly appreciated, even if it is to suggest another way to do the stats!
>> 
>> Thanks a lot, Vitória
>> 
>> 
>> _______________________________________________
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>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> -- 
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour 
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen 
> Neuronal Oscillations Group
> FieldTrip Development Team
> 
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
> 
> Contact:
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> Tel:    +31-(0)24-36-68493
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> 
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