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

Azeez Adebimpe ayobimpe2004 at hotmail.com
Sun Jan 26 10:43:58 CET 2014


Hi Chaitanya ,
I would suggest you try analyitcs instead of montecarlo  and use stat= ft_sourcestatitics(cfg, source1a, source2a .................., source1b,source2b.............);a and b are for the conditions. 
Azeez Adebimpe


Date: Sun, 26 Jan 2014 09:46:03 +0100
From: chaitanya.pro at gmail.com
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] Urgent: Error in Source Statistics, Group level

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 :)

===============================================



Best RegardsChaitanya Srinivas Lanka 


Wiss. Mitarbeiter                                       PhD Student

Functional and Restorative Neurosurgery Neural Information Processing
Neurosurgical 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

===============================================



Best RegardsChaitanya Srinivas Lanka 




Wiss. Mitarbeiter                                       PhD Student



Functional and Restorative Neurosurgery Neural Information Processing
Neurosurgical 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);



















===============================================







Best RegardsChaitanya Srinivas Lanka 

Wiss. Mitarbeiter                                       PhD Student





Functional and Restorative Neurosurgery Neural Information Processing
Neurosurgical 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
===============================================









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