Hi Katie,
On Feb 19, 2013, at 13:57 , Katie Bettencourt wrote:
> 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.
Well replace 1e6 by 1e18 then? Just to get it going and then compare
the result for this single run for both time window analyses?
best
Sebastian
>
> 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
> <[email protected]> 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
> fax: 626-395-8826
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> 1200 East California Boulevard
> CA 91125, Pasadena
> USA
>
>
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>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
--
Sebastian Moeller
telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616
fax: 626-395-8826
German GSM: +49 - 15 77 - 1 90 31 41
mobile: +1-626-325-8598
+1-626-807-5242
US CDMA: +1-626-807-5242
[email protected]
Division of Biology
MC 114-96
California Institute of Technology
1200 East California Boulevard
CA 91125, Pasadena
USA
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