<p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p><div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Hai list,</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><span style="color:rgb(29,28,29);font-family:Slack-Lato,appleLogo,sans-serif;font-size:15px;font-variant-ligatures:common-ligatures;background-color:rgb(248,248,248)">while computing the spatio-temporal clustering on power generated from 19 subject whole brain volume (after morphing), we observed two problems.</span> <br></div><div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">1. <span style="background-color:rgb(248,248,248);color:rgb(29,28,29);font-family:Slack-Lato,appleLogo,sans-serif;font-size:15px;font-variant-ligatures:common-ligatures">as the p_threshold is decreased there should be the less number of clusters. In our case its reverse. why?</span><span style="background-color:rgb(248,248,248);color:rgb(29,28,29);font-family:Slack-Lato,appleLogo,sans-serif;font-size:15px;font-variant-ligatures:common-ligatures"> refer the table</span></div><table border="0" cellpadding="0" cellspacing="0" width="896" style="border-collapse:collapse;width:538pt">
<colgroup><col width="299" span="3" style="width:179pt">
</colgroup><tbody><tr height="69" style="height:41.64pt">
<td height="69" class="gmail-oa1" width="299" style="height:41.64pt;width:179pt;border-width:1pt 1pt 3pt;border-style:solid;border-color:white;background:rgb(68,114,196);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri;color:white;font-weight:bold">P_threshold</span></p>
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<td class="gmail-oa1" width="299" style="width:179pt;border-width:1pt 1pt 3pt;border-style:solid;border-color:white;background:rgb(68,114,196);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri;color:white;font-weight:bold">F_threshold</span></p>
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<td class="gmail-oa1" width="299" style="width:179pt;border-width:1pt 1pt 3pt;border-style:solid;border-color:white;background:rgb(68,114,196);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri;color:white;font-weight:bold">Number of clusters (p<0.05)</span></p>
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<tr height="40" style="height:24.13pt">
<td height="40" class="gmail-oa2" width="299" style="height:24.13pt;width:179pt;border-width:3pt 1pt 1pt;border-style:solid;border-color:white;background:rgb(207,213,234);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">10</span><span style="font-size:18pt;font-family:Calibri;vertical-align:super">-2</span></p>
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<td class="gmail-oa2" width="299" style="width:179pt;border-width:3pt 1pt 1pt;border-style:solid;border-color:white;background:rgb(207,213,234);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">2.22</span></p>
</td>
<td class="gmail-oa2" width="299" style="width:179pt;border-width:3pt 1pt 1pt;border-style:solid;border-color:white;background:rgb(207,213,234);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">0</span></p>
</td>
</tr>
<tr height="40" style="height:24.13pt">
<td height="40" class="gmail-oa3" width="299" style="height:24.13pt;width:179pt;border:1pt solid white;background:rgb(233,235,245);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="line-height:normal;margin:0pt 0in;text-indent:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">10</span><span style="font-size:18pt;font-family:Calibri;vertical-align:super">-3</span></p>
</td>
<td class="gmail-oa3" width="299" style="width:179pt;border:1pt solid white;background:rgb(233,235,245);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">3.56</span></p>
</td>
<td class="gmail-oa3" width="299" style="width:179pt;border:1pt solid white;background:rgb(233,235,245);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">0</span></p>
</td>
</tr>
<tr height="40" style="height:24.13pt">
<td height="40" class="gmail-oa4" width="299" style="height:24.13pt;width:179pt;border:1pt solid white;background:rgb(207,213,234);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="line-height:normal;margin:0pt 0in;text-indent:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">10</span><span style="font-size:18pt;font-family:Calibri;vertical-align:super">-4</span></p>
</td>
<td class="gmail-oa4" width="299" style="width:179pt;border:1pt solid white;background:rgb(207,213,234);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">5.22</span></p>
</td>
<td class="gmail-oa4" width="299" style="width:179pt;border:1pt solid white;background:rgb(207,213,234);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">0</span></p>
</td>
</tr>
<tr height="40" style="height:24.13pt">
<td height="40" class="gmail-oa3" width="299" style="height:24.13pt;width:179pt;border:1pt solid white;background:rgb(233,235,245);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="line-height:normal;margin:0pt 0in;text-indent:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">10</span><span style="font-size:18pt;font-family:Calibri;vertical-align:super">-5</span></p>
</td>
<td class="gmail-oa3" width="299" style="width:179pt;border:1pt solid white;background:rgb(233,235,245);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">7.34</span></p>
</td>
<td class="gmail-oa3" width="299" style="width:179pt;border:1pt solid white;background:rgb(233,235,245);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">1</span></p>
</td>
</tr>
<tr height="40" style="height:24.13pt">
<td height="40" class="gmail-oa4" width="299" style="height:24.13pt;width:179pt;border:1pt solid white;background:rgb(207,213,234);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="line-height:normal;margin:0pt 0in;text-indent:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">10</span><span style="font-size:18pt;font-family:Calibri;vertical-align:super">-6</span></p>
</td>
<td class="gmail-oa4" width="299" style="width:179pt;border:1pt solid white;background:rgb(207,213,234);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">10.05</span></p>
</td>
<td class="gmail-oa4" width="299" style="width:179pt;border:1pt solid white;background:rgb(207,213,234);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">1</span></p>
</td>
</tr>
<tr height="40" style="height:24.13pt">
<td height="40" class="gmail-oa3" width="299" style="height:24.13pt;width:179pt;border:1pt solid white;background:rgb(233,235,245);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="line-height:normal;margin:0pt 0in;text-indent:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">10</span><span style="font-size:18pt;font-family:Calibri;vertical-align:super">-7</span></p>
</td>
<td class="gmail-oa3" width="299" style="width:179pt;border:1pt solid white;background:rgb(233,235,245);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">13.55</span></p>
</td>
<td class="gmail-oa3" width="299" style="width:179pt;border:1pt solid white;background:rgb(233,235,245);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">1</span></p>
</td>
</tr>
<tr height="40" style="height:23.8pt">
<td height="40" class="gmail-oa4" width="299" style="height:23.8pt;width:179pt;border:1pt solid white;background:rgb(207,213,234);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="line-height:normal;margin:0pt 0in;text-indent:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">10</span><span style="font-size:18pt;font-family:Calibri;vertical-align:super">-8</span></p>
</td>
<td class="gmail-oa4" width="299" style="width:179pt;border:1pt solid white;background:rgb(207,213,234);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">18.05</span></p>
</td>
<td class="gmail-oa4" width="299" style="width:179pt;border:1pt solid white;background:rgb(207,213,234);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">4</span></p>
</td>
</tr>
<tr height="40" style="height:23.8pt">
<td height="40" class="gmail-oa3" width="299" style="height:23.8pt;width:179pt;border:1pt solid white;background:rgb(233,235,245);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="line-height:normal;margin:0pt 0in;text-indent:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">10</span><span style="font-size:18pt;font-family:Calibri;vertical-align:super">-9</span></p>
</td>
<td class="gmail-oa3" width="299" style="width:179pt;border:1pt solid white;background:rgb(233,235,245);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">23.85</span></p>
</td>
<td class="gmail-oa3" width="299" style="width:179pt;border:1pt solid white;background:rgb(233,235,245);vertical-align:top;padding:3.6pt 7.2pt;color:windowtext;font-size:18pt;font-family:Arial">
<p style="margin-top:0pt;margin-bottom:0pt;margin-left:0in;direction:ltr;unicode-bidi:embed;word-break:normal"><span style="font-size:18pt;font-family:Calibri">3</span></p>
</td>
</tr>
</tbody></table><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">2. <span style="color:rgb(29,28,29);font-family:Slack-Lato,appleLogo,sans-serif;font-size:15px;font-variant-ligatures:common-ligatures;background-color:rgb(248,248,248)">each time the clusters are localised at different regions.</span><span style="font-family:Arial,Helvetica,sans-serif"></span></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><span style="color:rgb(29,28,29);font-family:Slack-Lato,appleLogo,sans-serif;font-size:15px;font-variant-ligatures:common-ligatures;background-color:rgb(248,248,248)">Can any one us say what is cause of this problem?</span></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><span style="color:rgb(29,28,29);font-family:Slack-Lato,appleLogo,sans-serif;font-size:15px;font-variant-ligatures:common-ligatures;background-color:rgb(248,248,248)">please refer to the snippet below, </span></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><pre class="gmail-c-mrkdwn__pre" style="box-sizing:inherit;margin-top:4px;margin-bottom:4px;padding:8px;font-size:12px;line-height:1.50001;font-variant-ligatures:none;white-space:pre-wrap;word-break:normal;border-radius:4px;color:rgb(29,28,29);font-family:Monaco,Menlo,Consolas,"Courier New",monospace">src_fs = mne.setup_volume_source_space( 'fsaverage', pos=5.,mri=aseg_fname, subjects_dir=subjects_dir,verbose=True)<br style="box-sizing:inherit">connectivity=spatial_src_connectivity(src_fs)<br style="box-sizing:inherit">power_test=np.zeros((2,n_subjects,n_vertices,n_timepoints)) ## here we are checking the power values are significant with respect to baseline, so the first sample is zero and the second sample is the contrast.<br style="box-sizing:inherit">contrast=l_gamma_power_dist8-l_gamma_power_dist1 ## l_gamma_power_dist8 and l_gamma_power_dist1 are the power generated for whole brain volume (after morphing) for n_subjects using Hilbert beamforming [contrast.shape=n_subjects,n_vertices,n_timepoints] <br style="box-sizing:inherit">power_test[1,:,:,:]=contrast<br style="box-sizing:inherit">p_accept = 0.05<br style="box-sizing:inherit">power_test=np.transpose(power_test,[0,1,3,2]) ## to rearrange the dimension 2 x n_subjects x n_timepoints x n_vertices<br style="box-sizing:inherit">p_threshold=10e-5<br style="box-sizing:inherit">n_subjects=19<br style="box-sizing:inherit">f_threshold=stats.distributions.f.ppf(1.-p_threshold/2.,n_subjects-1,n_subjects-1) <br style="box-sizing:inherit">cluster_stats = spatio_temporal_cluster_test(power_test, n_permutations=1000,connectivity=connectivity,<br style="box-sizing:inherit"> threshold=f_threshold, tail=1,seed=8, <br style="box-sizing:inherit"> n_jobs=1)<span class="gmail-c-mrkdwn__br" style="box-sizing:inherit;display:block;height:unset"></span>T_obs, clusters, p_values, _ = cluster_stats<br style="box-sizing:inherit">good_cluster_inds = np.where(p_values < p_accept)[0] <br style="box-sizing:inherit">for i_clu, clu_idx in enumerate(good_cluster_inds):<br style="box-sizing:inherit"> # unpack cluster information, get unique indices<br style="box-sizing:inherit"> time_inds, space_inds = np.squeeze(clusters[clu_idx])<br style="box-sizing:inherit"> time_inds = np.unique(time_inds)<br style="box-sizing:inherit"> space_inds = np.unique(space_inds)</pre><pre class="gmail-c-mrkdwn__pre" style="box-sizing:inherit;margin-top:4px;margin-bottom:4px;padding:8px;font-size:12px;line-height:1.50001;font-variant-ligatures:none;white-space:pre-wrap;word-break:normal;border-radius:4px;color:rgb(29,28,29);font-family:Monaco,Menlo,Consolas,"Courier New",monospace"><br></pre></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><span style="color:rgb(29,28,29);font-family:Slack-Lato,appleLogo,sans-serif;font-size:15px;font-variant-ligatures:common-ligatures;background-color:rgb(248,248,248)"><br></span></div><br></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr">Thank You<div>Pooja Prabhu</div><div><br></div></div></div></div></div></div>