Hmm, I think that might not help given that I get an XCond = 2.75109e+17
right before that error, so bumping to 6 probably isn't going to help.
I can't figure out why it is doing this now with just the change in
timewindow, but I'm obviously missing something. I actually only have 3
conditions in this experiment and 4 repetitions of each across the run
(which is the same as all the other runs that are working fine).
Katie
On Tue, Feb 19, 2013 at 4:46 PM, Sebastian Moeller <
sebastian.moell...@rwth-aachen.de> wrote:
> Hi Katie,
>
> what about just modifying the matlab code that gives the ill-conditioned
> error? So for free surfer 4.5 you will find in
> $FREESURFER_HOME/fsfast/toolbox/fast_selxavg3.m:
>
> XCond = cond(XtX);
> fprintf('XCond = %g (normalized)\n',XCond);
> if(XCond > 1e4)
> fprintf('ERROR: design is ill-conditioned\n');
> return;
> end
>
> While in freesurfer 5.1 it reads:
> XCond = cond(XtX);
> fprintf('XCond = %g (normalized)\n',XCond);
> if(XCond > 1e6)
> fprintf('ERROR: design is ill-conditioned\n');
> return;
> end
>
> So just try to change the threshold in fast_selxavg3.m to 1e6 and be done
> with (because if this works you are not doing any worse than you would do
> using free surfer 5.1). @Doug: Is that justifiable, or is 1e4 really the
> better threshold? (We have run into this issue in the past when we used
> very many conditions per run, and few repetitions of each condition per
> run).
>
>
> best regards
> sebastian
>
>
>
> On Feb 19, 2013, at 12:24 , Katie Bettencourt wrote:
>
> > I am having a problem with selxavg3-sess (for FS 4.5) where it is giving
> me an Ill-conditioned error that I can't trace out.
> >
> > I have 8 runs that I am running separately (same basic analysis for each
> run, but each run gets it's own analysis for svm purposes). Originally for
> this subject, I created an analysis and it ran fine for all 8 runs. I went
> back and changed the timewindow on the analysis (and only the timewindow)
> and now, while it runs fine for 7 or the 8 runs, one of them gives me an
> ill conditioned error during selxavg3-sess. I double checked the paradigm
> file and all conditions are listed, and the only change between when the
> analysis ran fine and when it gave me this error was changing the
> timewindow. The mkanalysis commands I used both times are listed below.
> >
> > Original analysis (worked fine):
> > foreach r (1 2 3 4 5 6 7 8)
> > mkanalysis-sess -analysis grating_nodist_ld_run${r} -TR 2 -paradigm
> grating.dat -designtype event-related -funcstem fmc -motioncor -runlistfile
> nodist_run${r}.txt -inorm -tpexclude tpexclude.dat -nconditions 3
> -timewindow 22 -TER 2 -noautostimdur -polyfit 2
> > end
> >
> > new analysis (illconditioned on one run only):
> > foreach r (1 2 3 4 5 6 7 8)
> > mkanalysis-sess -analysis grating_nodist_ld_34_run${r} -TR 2 -paradigm
> grating.dat -designtype event-related -funcstem fmc -motioncor -runlistfile
> nodist_run${r}.txt -inorm -tpexclude tpexclude.dat -nconditions 3
> -timewindow 34 -TER 2 -noautostimdur -polyfit 2
> > end
> >
> > Katie
> > _______________________________________________
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> >
> >
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> --
> Sebastian Moeller
>
> telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616
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>
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>
>
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