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

Chaitanya Srinivas chaitanya.pro at gmail.com
Sun Jan 26 09:46:03 CET 2014


Hi Eelke,

No significant results then in my data. I wonder how my boss takes it :P.
Anyway, thanks for your help on a Sunday that too.
>From your reply I also understand that the code doesn't have any mistakes :)

*===============================================*


*[image: Inline image 1]*
*Best Regards*


*Chaitanya Srinivas Lanka Wiss. Mitarbeiter
                                      *

*PhD StudentFunctional 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 9:40 AM, Eelke Spaak <eelke.spaak at donders.ru.nl>wrote:

> 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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>>
>>
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