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 <gr...@nmr.mgh.harvard.edu>
To: Leila Reddy <le...@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, 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<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
-- Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
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