---

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, 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
>
>
> ------------------------------------------------------------------------
>
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422

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