[FieldTrip] Urgent: Error in Source Statistics, Group level

[Eelke Spaak]

Hi Chaitanya,

stat.prob reflects the 'p-values' resulting from your statistical test. So
voxels expressing e.g. stat.prob < 0.05 should be considered reflecting a
significant difference between conditions. The NaNs correspond to voxels
outside the brain.

Since stat.mask is all zeros (which by default is just stat.prob < 0.05),
this indicates there are no significant differences between your
conditions. There is nothing we can help you with in this respect :)

Best,
Eelke


On 26 January 2014 09:06, Chaitanya Srinivas <chaitanya.pro at gmail.com>wrote:

> Hi Eelke,
>
>          I looked at the stat.stat values if that is what you mean. There
> are some NaNs , but also some values. Similarly in stat.prob, there are
> some 1's. The stat.mask is all zeros as you say.
>
> Any further suggestions from you?
> Thank you
>
> *=============================================== *
>
>
> *[image: Inline image 1]*
> *Best Regards*
>
>
> *Chaitanya Srinivas Lanka Wiss. Mitarbeiter
>                                       *
>
> *PhD Student Functional and Restorative Neurosurgery Neural Information
> ProcessingNeurosurgical University Hospital*
>
> *             Graduate Training Center for Neuroscience  Eberhard Karls
> University                          Eberhard Karls University **Otfried-Mueller-Str.45
> Österbergstr. 3*
> *  D-72076 Tuebingen                                    **D-72074
> Tuebingen*
>
> *Mobile Phone Number : +49-176-79035731*
> *===============================================*
>
>
> On Sun, Jan 26, 2014 at 8:53 AM, Eelke Spaak <eelke.spaak at donders.ru.nl>wrote:
>
>> Dear Chaitanya,
>>
>> Perhaps an obvious question: do you find any significant differences in
>> the statistics step (inspect the stat structure)? If not, the mask will
>> consist of all zeroes, hence giving you a 'blank' plot.
>>
>> Best,
>> Eelke
>>
>>
>> On 26 January 2014 08:46, Chaitanya Srinivas <chaitanya.pro at gmail.com>wrote:
>>
>>> Dear fieldtrip users,
>>> I would like to do sourcestatistics on a group level with eeg data. I have a
>>> pre and post intervention measurement for each of my 10 subjects
>>> . After source reconstruction using an DICS beamformer
>>> and volume normalization, I calculated the sourcegrandaverage for the pre and
>>> post condition and i have avg.pow for each subject.
>>>
>>>  However, when I use the grandaverage results in ft_sourcestatistics in the
>>> configuration shown below and plot the result I just get a blank anatomical
>>> mri. It only runs with cfg.parameter="pow" .I tried with cfg.parameter = 'avg.pow' it doesnt run.
>>> Do I have to set any additional parameters or am I making some mistake?
>>>
>>>
>>> cfg=[];
>>> cfg.dim         = grandAVGsourcePre.dim;
>>> cfg.method      = 'montecarlo';
>>> cfg.statistic   = 'depsamplesT';
>>> cfg.parameter   = 'pow';
>>> cfg.correctm    = 'cluster';
>>> cfg.numrandomization = 1000;
>>> cfg.alpha       = 0.05;
>>> cfg.tail        = 0;
>>>
>>> nsubj=length(sourcePre.trial);
>>> cfg.design(1,:) = [1:nsubj 1:nsubj];
>>> cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2];
>>> cfg.uvar        = 1;
>>> cfg.ivar        = 2;
>>> stat = ft_sourcestatistics(cfg, grandAVGsourcePre, grandAVGsourcePost);
>>>
>>>
>>> *and next interpolation*
>>>  cfg                                       = [];
>>>
>>>
>>>
>>>  cfg.voxelcoord                      = 'no';
>>>  cfg.parameter                       = 'mask';
>>>  cfg.interpmethod                   = 'nearest';
>>>  cfg.coordsys                        = 'mni';
>>>
>>>
>>>
>>>  mask                                  = ft_sourceinterpolate(cfg,stat,mri);
>>>  statplot.mask                      = mask.mask;
>>>
>>>
>>> *and then for plotting*
>>>
>>>
>>>
>>> cfg = [];
>>> cfg.method        = 'slice';
>>> cfg.funparameter  = 'stat';
>>> cfg.maskparameter = 'mask';
>>>    cfg.funcolorlim   = [-0.1 0.1];
>>>    cfg.opacitylim    = [-0.1 0.1];
>>> figure
>>> ft_sourceplot(cfg, statplot);
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> * ===============================================*
>>>
>>>
>>> *[image: Inline image 1]*
>>> *Best Regards*
>>>
>>>
>>> *Chaitanya Srinivas Lanka Wiss. Mitarbeiter
>>>                                       *
>>>
>>> *PhD Student Functional and Restorative Neurosurgery Neural Information
>>> ProcessingNeurosurgical University Hospital*
>>>
>>> *             Graduate Training Center for Neuroscience  Eberhard Karls
>>> University                          Eberhard Karls University **Otfried-Mueller-Str.45
>>> Österbergstr. 3*
>>> *  D-72076 Tuebingen                                    **D-72074
>>> Tuebingen*
>>>
>>> *Mobile Phone Number : +49-176-79035731*
>>> *===============================================*
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
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