Hi Doug,
I couldn't find a -no-whiten option in the usage for either selxavg-sess or selxavg3-sess. In any case, when I run the selxavg command, the screen output says: INFO: WhitenFlag = 0 (so I guess it's not whitening?).
I also looked for spikes or artifacts as you suggested and the main thing that struck me is that for the two subjects for whom I get this error, the min value in the 4D vol is 0 whereas for the 2 subjects that don't have this error, the min(vol) is non-zero (negative values in one subject and non-zero, positive for the other). Otherwise the amplitude profiles look pretty similar for all subjects. Could this be a divide by zero error somewhere in selxavg? And is there some way around it?
Thanks in advance, Leila
________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Leila Reddy leils@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu Sent: Fri, March 12, 2010 8:12:54 PM Subject: Re: [Freesurfer] selxavg error
hmmm, something is going wrong with the whitening. Can you try it without whitening? Also, look in the 4d volume for some artifact (eg, a spike). This might account for it.
doug
Leila Reddy wrote:
Hi,
I'm running into an error with selxavg ('Input to SVD must not contain NaN or Inf') that has been posted before on the mailing list but I couldn't find a solution to it.
The command was selxavg-sess -sf sessid -df sessdir -analysis loc-sm3. The output of the log file is: selxavg-sess log file $Id: selxavg-sess,v 1.15 2006/01/06 02:37:22 greve Exp $ uid=502(lreddy) gid=502(lreddy) groups=502(lreddy), 81(appserveradm), 79(appserverusr), 80(admin) /Volumes/donnees/GR/gr_analysis/kan_gr_006 /Applications/freesurfer/fsfast/bin/selxavg-sess -sf sessid -df sessdir -analysis loc-sm3 Darwin g5-leila.local 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386 Fri Mar 12 17:07:53 CET 2010 selxavg: Command not found.
/Volumes/donnees/GR/gr_data/kan_gr_006 Fri Mar 12 17:07:53 CET 2010
/Volumes/donnees/GR/gr_data/kan_gr_006/bold selxavg2 -TR 2.0000 -parname loc.para -o loc-sm3/h -i 018/fmc-sm3 -i 019/fmc-sm3 -i 020/fmc-sm3 -cfg /Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg -ipr 1.40625 -pomnibus loc-sm3/omnibus/fsig -fomnibus loc-sm3/omnibus/f
cat: /Applications/freesurfer/fsfast/docs/version: No such file or directory --- Parsing Config File: /Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg ---- -gammafit 2.25 1.25 -timewindow 30 -prestim 6 -polyfit 1 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 Logfile is loc-sm3/h_sxa.log matlab file is /tmp/sxa_5739.m ----------- Matlab file -------------- % Matlab file for selxavg2 Fri Mar 12 17:07:53 CET 2010 % This file may be deleted % /tmp/sxa_5739.m global QuitOnError; QuitOnError = 1; r = fast_selxavg( '-TR', '2.0000', '-parname', 'loc.para', '-o', 'loc-sm3/h', '-i', '018/fmc-sm3', '-i', '019/fmc-sm3', '-i', '020/fmc-sm3', '-cfg', '/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg', '-ipr', '1.40625', '-pomnibus', 'loc-sm3/omnibus/fsig', '-fomnibus', 'loc-sm3/omnibus/f'); if(r==0) fmri_touch('/Volumes/donnees/GR/gr_data/kan_gr_006/bold/loc-sm3/selxavg.ok.5739'); end qoe;
------- matlab output -------------------- Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen.
< M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.4.0.287 (R2007a) January 29, 2007Warning: Duplicate directory name: /Users/lreddy/matlab. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.comhttp://www.mathworks.com.
> >> >> >> $Id: fast_selxavg.m,v 1.22.2.2 2006/09/29 21:54:40 greve Exp $
Parsing Arguments RescaleTarget = 1000 Checking Parameters AutoStimDur: 0 StimDur: Number of Runs: 3 Input Volume List 1 018/fmc-sm3 2 019/fmc-sm3 3 020/fmc-sm3 Input Pardigm File List 1 018/loc.para 2 019/loc.para 3 020/loc.para Output Volume loc-sm3/h F Omnibus Volume loc-sm3/omnibus/f Sig Omnibus Volume loc-sm3/omnibus/fsig TR 2.000000 TER 2.000000 Total Window 30 PreStim Window 6 Remove Baseline 1 Remove Trend 0 Remove QTrend 0 Rescale Target 1000 nSkip 0 InPlane Res 1.40625 FWHM 0 Hanning Radius 0 Time Offset 0 GammaFit 1 1 2.25 1.25 GammaFit Alpha: 2 SPM HRF: -1 Seg Brain/Air 1 SynthSeed 0 ExtReg File mcextreg NExtReg 3 ExtRegOrthog 0 firstslice 0 nslices 17 nyqreg 0 SynthSeed = 0 Conditions Found (4): 1 2 3 4 Run 1: 32 32 32 32 Run 2: 32 32 32 32 Run 3: 32 32 32 32 Slice 0, 9.3119e-05 -------------- First Pass (Accumulation), 0.000414148 Run 1/3, 0.000853017 Excluding 0 Points: Run 2/3, 0.622743 Excluding 0 Points: Run 3/3, 1.0841 Excluding 0 Points: Second Pass (Residual Error Estimation), 1.52296 ??? Error using ==> svd Input to SVD must not contain NaN or Inf.
Error in ==> cond at 40 s = svd(A);
Error in ==> fast_selxavg at 193 c = cond(SumXtWX);
??? Undefined function or variable 'r'.
quiting matlab
2010-03-12 17:08:05.047 MATLAB[5789] Process manager already initialized -- can't fully enable headless mode.
ERROR: fast_selxavg() failed\n
The output of bugr is FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5 Kernel info: Darwin 8.11.1 i386
Thanks in advance, Leila
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