Hi Leila, does it work if you change the -refeventdur to something larger (eg, 2)? doug
On 07/22/2013 06:11 AM, Leila Reddy wrote: > Hi, > > I am running into an error with fast_selxavg3 (NaN values in XtX). Other have > people reported similar problems on the mailing list and I've tried > implementing some of the suggestions (namely, using -nowhiten and checking > that all events exist in my paradigm file), but I can't get rid of the error. > > > I have an event-related design with very short events (duration of 1 screen > refresh = 16.6ms) presented at random intervals. The error only occurs for > the -gammafit and -spmhrf analyses and not for -fir. When I check the > Xtmp.mat there are indeed NaNs in the first 2 columns of the X matrix. The > commands I issue and the output of bugr are below.I attach the paradigm file > from one run of the experiment (there are 5 runs in all but I started > focusing on just one in order to troubleshoot). TR=2 and numTRs=172. > > > Any help would be much appreciated. > > Thanks in advance, > Leila > > > mkanalysis-sess -fsd bold -surface fsaverage lh -fwhm 3 -event-related > -paradigm VRpara.para -nconditions 1 -gammafit 2.25 1.25 -TR 2 -refeventdur > 0.016 -polyfit 2 -mcextreg -analysis TargDist-gammafit-sm3.lh -per-run -rlf > runlist -force -nowhiten > > mkcontrast-sess -analysis TargDist-gammafit-sm3.lh -contrast VR -a 1 > > selxavg3-sess -s $subj -analysis TargDist-gammafit-sm3.lh > > Error message: > ------------------------- > $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ > /APPLICATIONS/freesurfer/fsfast/toolbox/fast_selxavg3.m > /APPLICATIONS/freesurfer/fsfast/toolbox/fast_ldanaflac.m > /APPLICATIONS/freesurfer/matlab/MRIread.m > ------------------------- > outtop = /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF > Extension format = nii.gz > 1 VR.mat > nruns = 1 > autostimdur = > > > outanadir = > /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF/BT/bold/TargDist-gammafit-sm3.lh > Found 149786/163842 (91.4) voxels in mask > Creating Design Matrix > ... creation time = 0.005 sec > DoMCFit = 1 > ntptot = 172, nX = 7, DOF = 165 > Saving X matrix to > /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF/BT/bold/TargDist-gammafit-sm3.lh/Xtmp.mat > Error using svd > Input to SVD must not contain NaN or Inf. > > Error in cond (line 36) > s = svd(A); > > Error in fast_selxavg3 (line 279) > XCond = cond(XtX); > >>> ------------------------------------------ > ERROR: fast_selxavg3() failed\n > > > Output of bugr: > --------------------------------------------------------------------- > > FREESURFER_HOME: /APPLICATIONS/freesurfer > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > > Kernel info: Darwin 12.0.0 x86_64 > > --------------------------------------------------------------------- > > > _______________________________________________ > 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 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.
