<div dir="ltr">Dear David,<div><br></div><div>Thanks for the info.</div><div><br></div><div>I've fiddled with FieldTrip a bit and I think (but I'm not sure) that if cfg.correctm is set to any option other than 'cluster', it does not cluster across times and channels. But I'm still not sure what option for cfg.correctm will run Blair&Karniski method.</div><div><br></div><div>Thanks for the code and the toolbox. I will check my data later with your toolbox as well.</div><div><br></div><div>Best wishes,</div><div><br></div><div>Kamia</div></div><br><div class="gmail_quote"><div dir="ltr">On Fri, Sep 7, 2018 at 4:35 PM David Groppe <<a href="mailto:david.m.groppe@gmail.com">david.m.groppe@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">What you would need to do Kamia is to set the neighbors matrix to the identity matrix:</div><div dir="ltr"><br></div><div dir="ltr"><pre class="m_4869235577586562697gmail-code" style="box-sizing:border-box;overflow:auto;font-family:Menlo,Monaco,Consolas,"Courier New",monospace;font-size:13px;padding:9.5px;margin-top:0px;margin-bottom:10px;line-height:1.42857;word-break:break-all;word-wrap:break-word;color:rgb(51,51,51);background-color:rgb(245,245,245);border:1px solid rgb(204,204,204);border-radius:4px;white-space:pre-wrap">neighbours = ft_prepare_neighbours(cfg_neighb, dataFC_LP);</pre></div><div>That function is described here:</div><div dir="ltr"><a href="http://www.fieldtriptoolbox.org/reference/ft_prepare_neighbours" target="_blank">http://www.fieldtriptoolbox.org/reference/ft_prepare_neighbours</a><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">And I was wrong with what I initially told you. This will still cluster variables across time within single electrodes, so it is not equivalent to the Blair & Karniski test. I don't know if there is a way to prevent any clustering at all in FieldTrip (perhaps set the neighbour matrix to all zeros?).</div><div dir="ltr"><br></div><div dir="ltr">I have some MATLAB code that implements the Blair & Karniski method:</div><div dir="ltr"><br></div><div dir="ltr"><a href="https://www.mathworks.com/matlabcentral/fileexchange/54585-mult_comp_perm_t2-data1-data2-n_perm-tail-alpha_level-mu-t_stat-reports-seed_state?s_tid=prof_contriblnk" target="_blank">https://www.mathworks.com/matlabcentral/fileexchange/54585-mult_comp_perm_t2-data1-data2-n_perm-tail-alpha_level-mu-t_stat-reports-seed_state?s_tid=prof_contriblnk</a><br></div><div dir="ltr"><br></div><div dir="ltr"><a href="https://www.mathworks.com/matlabcentral/fileexchange/29782-mult_comp_perm_t1-data-n_perm-tail-alpha_level-mu-reports-seed_state?s_tid=prof_contriblnk" target="_blank">https://www.mathworks.com/matlabcentral/fileexchange/29782-mult_comp_perm_t1-data-n_perm-tail-alpha_level-mu-reports-seed_state?s_tid=prof_contriblnk</a><br></div><div dir="ltr"><br></div><div>That might be easier to use. It is part of a toolbox for ERP analysis that may be useful if you're working with ERPs:</div><div dir="ltr"><div><a href="https://openwetware.org/wiki/Mass_Univariate_ERP_Toolbox" target="_blank">https://openwetware.org/wiki/Mass_Univariate_ERP_Toolbox</a><br></div><div><br></div><div>cheers,</div><div> -David</div><div><br></div><div><br></div></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr">On Thu, Sep 6, 2018 at 3:35 PM Kamia Kavi <<a href="mailto:kamiakavi@gmail.com" target="_blank">kamiakavi@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><p class="m_4869235577586562697m_-5791275999350157062gmail-MsoNoSpacing" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">Hey David,</p>
<p class="m_4869235577586562697m_-5791275999350157062gmail-MsoNoSpacing" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"> </p>
<p class="m_4869235577586562697m_-5791275999350157062gmail-MsoNoSpacing" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">Thank you very much for your tip as well as your paper. I
printed that and will read it tomorrow.</p>
<p class="m_4869235577586562697m_-5791275999350157062gmail-MsoNoSpacing" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"> </p>
<p class="m_4869235577586562697m_-5791275999350157062gmail-MsoNoSpacing" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">Two follow-up questions:</p>
<p class="m_4869235577586562697m_-5791275999350157062gmail-MsoNoSpacing" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">1) So, to not cluster the timepoints/channels, is it enough
the change the ‘cfg.correcm’ parameter from ‘cluster’ to ‘no’ and leave the
other parameters unchanged?</p>
<p class="m_4869235577586562697m_-5791275999350157062gmail-MsoNoSpacing" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"> </p>
<p class="m_4869235577586562697m_-5791275999350157062gmail-MsoNoSpacing" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">2) if cfg.correctm = ‘no’ (and, of course, using cfg.method
= 'montecarlo'), are significant values (i.e., ones rather than zeros) in stat.mask
logical matrix already corrected for multiple comparisons? In other words, can
these ‘ones’ in the matrix be considered as statically significant channel/timepoints
between two conditions at a certain critical value?</p>
<p class="m_4869235577586562697m_-5791275999350157062gmail-MsoNoSpacing" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"> </p>
<p class="m_4869235577586562697m_-5791275999350157062gmail-MsoNoSpacing" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">Best wishes,</p>
<p class="m_4869235577586562697m_-5791275999350157062gmail-MsoNoSpacing" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"> </p>
<p class="m_4869235577586562697m_-5791275999350157062gmail-MsoNoSpacing" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">Kamia</p></div><br><div class="gmail_quote"><div dir="ltr">On Thu, Sep 6, 2018 at 7:35 PM David Groppe <<a href="mailto:david.m.groppe@gmail.com" target="_blank">david.m.groppe@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div dir="ltr"><div dir="ltr">Hi Kamia,<div> The cluster-based permutation test implemented by FieldTrip is similar to the Blair & Karniski method:</div><div><br></div><div><a href="http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock" target="_blank">http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock</a><br></div><div><br></div><div>If you set the parameters of the test such that no timepoint/electrode has any neighbours (i.e., you can't form any clusters), than it is equivalent to the Blair & Karniski method.</div><div><br></div><div>For an explanation of how the cluster-based test differs from Blair & Karniski, I cover that in this review/tutorial paper:</div><div><br></div><div><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4060794/" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4060794/</a><br></div><div><br></div><div>cheers,</div><div> -David</div><div><br></div><div><br></div></div></div></div><br><div class="gmail_quote"><div dir="ltr">On Thu, Sep 6, 2018 at 10:36 AM Kamia Kavi <<a href="mailto:kamiakavi@gmail.com" target="_blank">kamiakavi@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div dir="ltr">Dear FieldTrip-ers,<div><br></div><div>Is there an option in FirldTrip to perform a non-parametric statistics as described in Blair and Karniski 1993?</div><div><br></div><div>Best wishes,</div><div><br></div><div>Kamia</div></div></div>
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