An epiphany lead me to the solution to the problem, which I shall post here since I am apparently due to experience it again in 2019. The NAN values in the GLM matrices were the result of there being a condition that did not appear in any of the .par files across all of the runs. Once these files were edited so that all of conditions 1, 2 and 3 appeared somewhere among these files, selxavg3-sess was able to run.
/********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ <http://ccnlab.buffalo.edu/> * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/ > Hi Doug et al., > > It appears I've encountered this problem once before: > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-February/043647.html > > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-February/043647.html> > > Unfortunately there is no record of any resolution (if there was one) in the > original thread, and I have no recollection of what the outcome was. Where > the thread did leave off was a request for the Xtmp.mat file, so I will > include the Xtmp.mat file from the analysis that worked (GoodXtmp.mat) and > the one that failed (BadXtmp.mat). > > The error message: > > Creating Design Matrix > ... creation time = 0.019 sec > DoMCFit = 1 > ntptot = 2592, nX = 81, DOF = 2511 > Saving X matrix to /home/chris/SEM/FS_0231/bold/FAM.self.sm4.down.rh/Xtmp.mat > Error using svd > Input to SVD must not contain NaN or Inf. > Error in cond (line 35) > s = svd(A); > Error in fast_selxavg3 (line 279) > XCond = cond(XtX); > > Curiously, unless something was overlooked, the same analysis was carried out > on another dataset that went through the same preprocessing steps without > incident. > > The Xn matrix in BadXtmp.mat contains 3 columns of NaN (:,[7,8,9]), but > without knowing how those values are calculated, I can't take a principled > stab at fixing the problem. > > Thanks for your help, > Chris > > <GoodXtmp.mat><BadXtmp.mat> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline > <http://www.partners.org/complianceline> . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail.
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