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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