That means that your design matrix is ill-conditioned. This error means one of two things is wrong with your .par file (located in each run of each subjects bold directory): 1) there are not two or more occurrences of one of your conditions; or 2) there is a pattern to your conditions (for example condition 3 always follows condition 4). You can avoid this error message for the sake of analysis by 1) replacing other conditions with occurrences of your missing condition, so that each condition is represented at least twice; or 2) by changing your conditions so that they break the pattern at least twice. Even though the effect of this change is quite small, you should distribute the added conditions evenly across the other conditions. Ideally, however, you would alter your stimuli so that you do not get this error in the first place.
On 12/09/2015 02:19 PM, Christina Pressl wrote: > hi doug, > > thank you so much for your quick reply. > yes - I saw this error after I sent you the error log. > I checked the paradigm file, corrected it and rerun everything. > > now this error is gone but I still get the following: > > Error using svd > Input to SVD must not contain NaN or Inf. > Error in cond (line 36) > s = svd(A); > > Error in fast_selxavg3 (line254) > XCond = cond(XtX); > > >> - - - - - — - - — - - — - — - > > EROOR: fast_selxavg3() failed\n > > > > Your help is much appreciated > > > >> On Dec 9, 2015, at 1:57 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> >> Did you see the error description: >> >> ERROR: >> /space/mdeh5/1/halgdev/projects/christina/FSFAST/Project/NC211_fmri_060515/Sess01/bold/004/oddeven.par >> is not correctly formatted. Line 19 only has 0 items >> >> did you check this file? >> >> >> On 12/09/2015 12:38 PM, Christina Pressl wrote: >>> Dear Freesurfer Experts, >>> >>> I am having trouble with selxavg3-sess and was wondering if you could >>> maybe help me resolving the issue (error log attached) >>> >>> >>> I ran >>> >>> #preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run >>> >>> and the following commands for lh, rh and mni305 >>> >>> #mkanalysis-sess –fsd bold –stc up -surface fsaverage lh -fwhm 5 >>> -event-related -paradigm oddeven.par -nconditions 3 -spmhrf 0 -TR 2 >>> -refeventdur 10.750 -nskip 4 –mcextreg -polyfit 2 -analysis >>> oddeven.sm5.lh >>> >>> #mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-object –a >>> 1 –c 2 –c 3 >>> >>> #mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-fix –a >>> 1 –c 0 >>> >>> >>> >>> Thank you very much. >>> >>> Christina >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> 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 . 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. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
