<div dir="ltr">Hey Micha<span style="font-size:12.8px">ł</span>,<div><br></div><div>I think your problem lies within the use of <span style="font-size:12.8px">"ft_statfun_depsamplesT". FieldTrip then assumes that each trial index from condition one is paired with the same trial index from condition two which is why you get the output "</span><span style="font-size:12.8px">repeated measurement in variable 2 over 11 levels</span></div><div style="font-size:12.8px">number of repeated measurements in each level is 2 2 2 2 2 2 2 2 2 2 1 "</div><div style="font-size:12.8px">In your case the design matrix should only include your first row and no uvar, statfun being <span style="font-size:12.8px">ft_statfun_indepsamplesT.</span></div><div style="font-size:12.8px"><span style="font-size:12.8px">See: </span><a href="http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_freq#permutation_test" target="_blank" style="font-size:12.8px">http://www.fieldtriptoolbox.or<wbr>g/tutorial/cluster_permutation<wbr>_freq#permutation_test</a></div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">Cheers</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px"><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jan 24, 2017 at 3:21 PM, Michał Komorowski <span dir="ltr"><<a href="mailto:michak@is.umk.pl" target="_blank">michak@is.umk.pl</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Dear community,</div><div><br></div><div>Currently I am working on source analysis from EEG data. I have some trouble using ft_sourcestatistics do a between-trials analysis (single subject).</div><div>I am trying to compare source from trials from task type A (ctrl) to with trials from task type B (task). Mainly I rely on <a href="http://www.fieldtriptoolbox.org/example/source_statistics" target="_blank">http://www.fieldtriptoolbox.or<wbr>g/example/source_statistics</a> .</div><div><br></div><div>For almost week I am trying find a solution, inculding testing ft_sourcestatistics with different combinations of data:</div><div>1) source 1 : no ft_sourcedescriptives and no ft_sourceinterpolate used</div><div>2) source 2 : used ft_sourcedescriptives and no ft_sourceinterpolate used</div><div>3) source 3 : used ft_sourcedescriptives and used ft_sourceinterpolate</div><div><br></div><div>For cases 1) and 2) I get very similar errors "Invalid specification of the design array. Error using ft_statistics_montecarlo (line 242) could not determine the parametric critical value for clustering" (full error messages at the bottom). In case 3) I cannot run ft_statistics because there are no trials anymore.</div><div>I have tried changing design matrix, search community messages for some advice and read related articles on fieldtriptoolbox site, but I have not find the answer.</div><div><br></div><div>Any help would be appreciated.</div><div><br></div><div>Michał Komorowski</div><div><br></div><div><br></div><div>Statistics code:</div><div><br></div><div>cfg = [];</div><div>%cfg.dim = source.dim; % there is no such field in the data</div><div>cfg.method = 'montecarlo';</div><div>cfg.statistic = 'ft_statfun_depsamplesT';</div><div>cfg.parameter = 'pow';</div><div>cfg.correctm = 'cluster';</div><div>cfg.numrandomization = 100;</div><div>cfg.alpha = 0.05;</div><div>cfg.correcttail = 'alpha'; % <a href="http://www.fieldtriptoolbox.org/faq/why_should_i_use_the_cfg.correcttail_option_when_using_statistics_montecarlo" target="_blank">http://www.fieldtriptoolbox.or<wbr>g/faq/why_should_i_use_the_cfg<wbr>.correcttail_option_when_using<wbr>_statistics_montecarlo</a></div><div>cfg.tail = 0; % two sided test</div><div>cfg.design(1,:) = design; % condition code</div><div>cfg.design(2,:) = [1:length(find(design==1)) 1:length(find(design==2))]; % trial indices</div><div>cfg.uvar = 2; % unit of observation variable: trials</div><div>cfg.ivar = 1; % independent variable: condition code</div><div>% I think design matrix is ok according to: <a href="http://www.fieldtriptoolbox.org/walkthrough#paired_comparison" target="_blank">http://www.fieldtriptoolbox.or<wbr>g/walkthrough#paired_compariso<wbr>n</a>)</div><div><br></div><div>stat = ft_sourcestatistics(cfg, source);</div><div><br></div><div><br></div><div><br></div><div><br></div><div>Data structures and error messages </div><div><br></div><div>Case 1) no ft_sourcedescriptives and no ft_sourceinterpolate used</div><div><br></div><div>source = </div><div><br></div><div> freq: 10</div><div> cumtapcnt: [21x1 double]</div><div> inside: [231420x1 logical]</div><div> pos: [231420x3 double]</div><div> method: 'rawtrial'</div><div> trial: [1x21 struct]</div><div> df: 21</div><div> cfg: [1x1 struct]</div><div><br></div><div>the call to "ft_selectdata" took 1 seconds</div><div>using "ft_statistics_montecarlo" for the statistical testing</div><div>using connectivity of voxels in 3-D volume</div><div>using "ft_statfun_depsamplesT" for the single-sample statistics</div><div>constructing randomized design</div><div>total number of measurements = 21</div><div>total number of variables = 2</div><div>number of independent variables = 1</div><div>number of unit variables = 1</div><div>number of within-cell variables = 0</div><div>number of control variables = 0</div><div>using a permutation resampling approach</div><div>repeated measurement in variable 2 over 11 levels</div><div>number of repeated measurements in each level is 2 2 2 2 2 2 2 2 2 2 1 </div><div>computing a parametric threshold for clustering</div><div>Error using ft_statfun_depsamplesT (line 84)</div><div>Invalid specification of the design array.</div><div>Error using ft_statistics_montecarlo (line 242)</div><div>could not determine the parametric critical value for clustering</div><div><br></div><div>Error in ft_sourcestatistics (line 205)</div><div> [stat, cfg] = statmethod(cfg, dat, design);</div><div> </div><div>>> cfg.design</div><div><br></div><div>ans =</div><div><br></div><div> 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2</div><div> 1 2 3 4 5 6 7 8 9 10 11 1 2 3 4 5 6 7 8 9 10</div><div><span class="m_4634959913525831993m_4190330521700362147gmail-m_-1136596011051824820m_1302007016799592746gmail-Apple-tab-span" style="white-space:pre-wrap"> </span> </div><div><span class="m_4634959913525831993m_4190330521700362147gmail-m_-1136596011051824820m_1302007016799592746gmail-Apple-tab-span" style="white-space:pre-wrap"> </span> </div><div><span class="m_4634959913525831993m_4190330521700362147gmail-m_-1136596011051824820m_1302007016799592746gmail-Apple-tab-span" style="white-space:pre-wrap"> </span> </div><div>Case 2) used ft_sourcedescriptives and no ft_sourceinterpolate used</div><div><br></div><div>source_app = </div><div><br></div><div> freq: 10</div><div> cumtapcnt: [21x1 double]</div><div> inside: [231420x1 logical]</div><div> pos: [231420x3 double]</div><div> method: 'rawtrial'</div><div> trial: [1x21 struct]</div><div> df: 21</div><div> cfg: [1x1 struct]</div><div><br></div><div>the call to "ft_selectdata" took 0 seconds</div><div>using "ft_statistics_montecarlo" for the statistical testing</div><div>using connectivity of voxels in 3-D volume</div><div>using "ft_statfun_depsamplesT" for the single-sample statistics</div><div>constructing randomized design</div><div>total number of measurements = 21</div><div>total number of variables = 2</div><div>number of independent variables = 1</div><div>number of unit variables = 1</div><div>number of within-cell variables = 0</div><div>number of control variables = 0</div><div>using a permutation resampling approach</div><div>repeated measurement in variable 2 over 11 levels</div><div>number of repeated measurements in each level is 2 2 2 2 2 2 2 2 2 2 1 </div><div>computing a parametric threshold for clustering</div><div>Error using ft_statfun_depsamplesT (line 84)</div><div>Invalid specification of the design array.</div><div>Error using ft_statistics_montecarlo (line 242)</div><div>could not determine the parametric critical value for clustering</div><div><br></div><div>Error in ft_sourcestatistics (line 205)</div><div> [stat, cfg] = statmethod(cfg, dat, design);</div><div><br></div><div> </div><div> </div><div>Case 3) used ft_sourcedescriptives and used ft_sourceinterpolate</div><div><br></div><div>source_mri_align_ctrl = </div><div><br></div><div> freq: 10</div><div> anatomy: [128x128x128 double]</div><div> coordsys: 'spm'</div><div> dim: [128 128 128]</div><div> pos: [2097152x3 double]</div><div> transform: [4x4 double]</div><div> unit: 'mm'</div><div> inside: [128x128x128 logical]</div><div> pow: [2097152x1 double]</div><div> cfg: [1x1 struct]</div><div><span class="m_4634959913525831993m_4190330521700362147gmail-m_-1136596011051824820m_1302007016799592746gmail-Apple-tab-span" style="white-space:pre-wrap"> </span> </div><div>% there is no trials so one cannot conduct between-trials statistics ...</div></div>
<br>______________________________<wbr>_________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a><br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">https://mailman.science.ru.nl/<wbr>mailman/listinfo/fieldtrip</a><br></blockquote></div><br></div></div>