Ah, the subject was missing Neutral from all three runs. Removing them from the sessid gets rid of the error.
Thanks! Keith -- Keith Yoder PhD Student, Integrative Neuroscience Social Cognitive Neuroscience Laboratory The University of Chicago 5846 S. University Avenue, Kelly 312 Chicago, IL 60637 Phone: 574-215-9678 kjyo...@uchicago.edu On Fri, Dec 7, 2012 at 2:05 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > Hi Keith, > if you don't have any Neutral in a session, you can't do a Good-Neutral > comparison. If you have multiple runs within a session, then it should be > ok. > doug > > > On 12/07/2012 03:02 PM, Keith Yoder wrote: > >> Hi Doug, >> >> I'm having a similar problem. Subjects had the opportunity to classify >> stimuli into one of three categories (Good, Bad, Neutral). For some >> subjects, one of more of the runs did not contain any stimuli that they >> classified as Neutral. If I want to look at a contrast that compare >> Good-Neutral, how should I go about doing this with FS-FAST? I'd like to >> keep the runs that contained neutral classifications for those subjects, >> but if I have to throw out those subjects to get the contrast, I guess I >> could. >> >> Thanks, >> Keith >> -- >> Keith Yoder >> PhD Student, Integrative Neuroscience >> Social Cognitive Neuroscience Laboratory >> The University of Chicago >> 5846 S. University Avenue, Kelly 312 >> Chicago, IL 60637 >> Phone: 574-215-9678 >> kjyo...@uchicago.edu <mailto:kjyo...@uchicago.edu> >> >> >> >> >> >> On Thu, Mar 1, 2012 at 2:27 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>> >> wrote: >> >> If you have an event type for which there is no event, then that is >> definitely the problem. Let me know if it is not that. >> doug >> >> Sid Kundu wrote: >> > It is attached. Finn mentioned it may be due to an event number >> being >> > missing from the particular subject, which could be possible in the >> > analysis I am doing. >> > ______________________________**___ >> > Sid Kundu >> > Biomedical Engineering >> > Boston University >> > >> > >> > >> > On Thu, Mar 1, 2012 at 11:15 AM, Douglas N Greve >> > <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>>> >> wrote: >> > >> > It's probably a problem with your design. Can you send me the >> > Xtmp.mat file? >> > doug >> > >> > >> > Sid Kundu wrote: >> > >> > Hi Doug, >> > >> > I created a new first level analysis along with new >> contrasts >> > and event numbers for a group of subjects I had previously >> > done analyses on. All but one of the subjects finished >> > selxavg3 without error, but one subject gave the >> following error: >> > >> > >> > Saving X matrix to >> > >> /home/sidkundu/freesurfer/**sessions/Heading-TTP/LMV2010_** >> N19_Heading-TTP/bold/TTP-**analysis-3/Xtmp.mat >> > Error using svd >> > Input to SVD must not contain NaN or Inf. >> > >> > Error in cond (line 39) >> > s = svd(A); >> > >> > Error in fast_selxavg3 (line 248) >> > XCond = cond(XtX); >> > >> ------------------------------**------------ >> > ERROR: fast_selxavg3() failed\n >> > >> > >> > I looked at the generated Xtmp.mat file and it shows the >> > design matrix X has all zeros in 2 columns, resulting in >> NaNs >> > in the same columns for Xn, and corresponding NaNs in >> XtX. I'm >> > wondering what would cause this or why it would only >> occur for >> > only one subject. >> > >> > ______________________________**___ >> > Sid Kundu >> > Biomedical Engineering >> > Boston University >> > >> > >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> > gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu><mailto: >> gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>> >> >> > Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 >> <tel:617-726-7422> >> > <tel:617-726-7422 <tel:617-726-7422>> >> >> > >> > Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> > >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> > FileDrop: >> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> > <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** >> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> > >> > >> > >> > 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. >> > >> > >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.** >> harvard.edu <Freesurfer@nmr.mgh.harvard.edu>> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > 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/ <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 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.
