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, 2007
Warning: Duplicate directory name: /Users/lreddy/matlab.
To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit 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
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.com http://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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Leila Reddy