<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Nick,<div class=""><br class=""></div><div class="">Thanks for the quick reply!</div><div class=""><br class=""></div><div class="">The problem is, when I run the searchlight without setting “corrcoef_only†to “Trueâ€, I get this error (here are the last few lines of the output, let me know if it doesn’t show up properly):</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">[SLC] DBG: +0:00:57 ======[100%]====== 0:00:00 ROI 1465 (1465/1465), 36 features</div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 19px;" class=""><br class=""></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">[SLC] DBG: hstacking 1465 results of shape (1, 2)</div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">[SLC] DBG: hstacked shape (1, 2930)</div><div style="margin: 0px; font-family: Monaco; color: rgb(195, 55, 32); background-color: rgb(0, 0, 0);" class="">---------------------------------------------------------------------------</div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #c33720" class="">ValueError</span> Traceback (most recent call last)</div><div style="margin: 0px; font-family: Monaco; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);" class=""><ipython-input-185-a11e1def05a0><span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> in </span><span style="font-variant-ligatures: no-common-ligatures; color: #34bbc7" class=""><module></span><span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">()</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class="">----> 1</span><span style="font-variant-ligatures: no-common-ligatures; color: #c33720" class=""> </span>slres <span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">=</span> sl<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(</span>ds<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">)</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 19px;" class=""><br class=""></div><div style="margin: 0px; font-family: Monaco; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);" class="">/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mvpa2/base/learner.pyc<span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> in </span><span style="font-variant-ligatures: no-common-ligatures; color: #34bbc7" class="">__call__</span><span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(self, ds)</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 256</span><span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> </span>"used and auto training is disabled."</div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 257</span> % str(self))</div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class="">--> 258</span><span style="font-variant-ligatures: no-common-ligatures; color: #c33720" class=""> </span><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class="">return</span> super<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(</span>Learner<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">,</span> self<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">).</span>__call__<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(</span>ds<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">)</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);" class=""> 259<span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> </span></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 260</span> is_trained = property(fget=lambda x: x.__is_trained, fset=_set_trained,</div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 19px;" class=""><br class=""></div><div style="margin: 0px; font-family: Monaco; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);" class="">/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mvpa2/base/node.pyc<span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> in </span><span style="font-variant-ligatures: no-common-ligatures; color: #34bbc7" class="">__call__</span><span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(self, ds, _call_kwargs)</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);" class=""> 135<span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> </span></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 136</span> self<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">.</span>_precall<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(</span>ds<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">)</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class="">--> 137</span><span style="font-variant-ligatures: no-common-ligatures; color: #c33720" class=""> </span>result <span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">=</span> self<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">.</span>_call<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(</span>ds<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">,</span> <span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">**(</span>_call_kwargs <span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class="">or</span> self<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">.</span>_get_call_kwargs<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(</span>ds<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">)))</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 138</span> result <span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">=</span> self<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">.</span>_postcall<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(</span>ds<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">,</span> result<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">)</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);" class=""> 139<span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> </span></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 19px;" class=""><br class=""></div><div style="margin: 0px; font-family: Monaco; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);" class="">/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mvpa2/measures/searchlight.pyc<span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> in </span><span style="font-variant-ligatures: no-common-ligatures; color: #34bbc7" class="">_call</span><span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(self, dataset)</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);" class=""> 152<span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> </span></div><div style="margin: 0px; font-family: Monaco; color: rgb(195, 55, 32); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 153</span><span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> </span># pass to subclass</div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class="">--> 154</span><span style="font-variant-ligatures: no-common-ligatures; color: #c33720" class=""> </span>results <span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">=</span> self<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">.</span>_sl_call<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(</span>dataset<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">,</span> roi_ids<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">,</span> nproc<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">)</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);" class=""> 155<span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> </span></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 156</span> <span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class="">if</span> <span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">'mapper'</span> <span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class="">in</span> dataset<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">.</span>a<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">:</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 19px;" class=""><br class=""></div><div style="margin: 0px; font-family: Monaco; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);" class="">/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mvpa2/measures/searchlight.pyc<span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> in </span><span style="font-variant-ligatures: no-common-ligatures; color: #34bbc7" class="">_sl_call</span><span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(self, dataset, roi_ids, nproc)</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 382</span> dataset<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">=</span>dataset<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">,</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 383</span> roi_ids<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">=</span>roi_ids<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">,</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(195, 55, 32); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class="">--> 384</span> results=self.__handle_all_results(p_results))</div><div style="margin: 0px; font-family: Monaco; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);" class=""> 385<span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> </span></div><div style="margin: 0px; font-family: Monaco; color: rgb(195, 55, 32); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 386</span><span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> </span># Assure having a dataset (for paranoid ones)</div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 19px;" class=""><br class=""></div><div style="margin: 0px; font-family: Monaco; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);" class="">/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mvpa2/measures/searchlight.pyc<span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> in </span><span style="font-variant-ligatures: no-common-ligatures; color: #34bbc7" class="">_concat_results</span><span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(sl, dataset, roi_ids, results)</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);" class=""> 262<span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> </span></div><div style="margin: 0px; font-family: Monaco; color: rgb(195, 55, 32); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 263</span><span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> </span># store the center ids as a feature attribute</div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class="">--> 264</span><span style="font-variant-ligatures: no-common-ligatures; color: #c33720" class=""> </span>result_ds<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">.</span>fa<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">['center_ids']</span> <span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">=</span> roi_ids</div><div style="margin: 0px; font-family: Monaco; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);" class=""> 265<span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> </span></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 266</span> <span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class="">return</span> result_ds</div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 19px;" class=""><br class=""></div><div style="margin: 0px; font-family: Monaco; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);" class="">/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mvpa2/base/collections.pyc<span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> in </span><span style="font-variant-ligatures: no-common-ligatures; color: #34bbc7" class="">__setitem__</span><span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(self, key, value)</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 597</span> len<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(</span>value<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">.</span>value<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">),</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 598</span> ulength<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">,</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(195, 55, 32); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class="">--> 599</span> str(self)))</div><div style="margin: 0px; font-family: Monaco; color: rgb(195, 55, 32); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 600</span><span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""> </span># tell the attribute to maintain the desired length</div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #34bd26" class=""> 601</span> value<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">.</span>set_length_check<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">(</span>ulength<span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">)</span></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); min-height: 19px;" class=""><br class=""></div><div style="margin: 0px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #c33720" class="">ValueError</span>: Collectable 'center_ids' with length [1465] does not match the required length [2930] of collection '<FeatureAttributesCollection: metrics>'.</div></div><div class=""><br class=""></div><div class="">Presumably there’s a clever way to get around this that I just haven’t figured out.</div><div class=""><br class="">
<br class=""><div><blockquote type="cite" class=""><div class="">On May 19, 2017, at 10:04 AM, Nick Oosterhof <<a href="mailto:n.n.oosterhof@googlemail.com" class="">n.n.oosterhof@googlemail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><br class=""><blockquote type="cite" class="">On 19 May 2017, at 15:58, William Graves <<a href="mailto:william.wyatt.graves@gmail.com" class="">william.wyatt.graves@gmail.com</a>> wrote:<br class=""><br class="">Dear PyMVPA Experts:<br class=""><br class="">In trying to do an RSA analysis using PyMVPA, I have to say your tools are really great. One issue I’ve run into though is that I can’t figure out from your documentation how to output both correlation coefficients and p-values into a NIfTI file to view the output.<br class=""><br class="">Here’s what I’ve done so far:<br class=""><br class="">Set up a comparison matrix for eventually testing against each searchlight:<br class="">tdm = rsa.pdist(ds.sa.orth, 'correlation’)<br class=""><br class="">Set up the target similarity comparison:<br class="">dsm = rsa.PDistTargetSimilarity(tdm, comparison_metric='spearman', corrcoef_only=True)<br class=""><br class="">Set up the searchlight:<br class="">sl = sphere_searchlight(dsm, radius=3, enable_ca='ca.pvalues’)<br class=""><br class="">Run it:<br class="">slres = sl(ds)<br class=""><br class="">And finally output the results in NIfTI format:<br class="">map2nifti(slres, imghdr=ds.a.imghdr).to_filename('meansubj.rsa_orth_sl.nii.gz’)<br class=""><br class="">From your documentation, it seems like there’s a way to output not only correlation coefficients for each voxel, but also p-values.<br class=""></blockquote><br class="">See <a href="http://www.pymvpa.org/generated/mvpa2.measures.rsa.PDistTargetSimilarity.html" class="">http://www.pymvpa.org/generated/mvpa2.measures.rsa.PDistTargetSimilarity.html</a><br class=""><br class="">corrcoef_only : bool, optional<br class="">If True, return only the correlation coefficient (rho), otherwise return rho and probability, p. Constraints: value must be convertible to type bool. [Default: False]<br class=""><br class=""><br class="">_______________________________________________<br class="">Pkg-ExpPsy-PyMVPA mailing list<br class=""><a href="mailto:Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org" class="">Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org</a><br class="">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa</div></blockquote></div><br class=""></div></body></html>