Re: [Freesurfer] selxavg3-sess illconditioned error

I don't know. It might be that the other ones are close to being badly conditioned and just don't meet my (arbitrary) threshold. doug

On 03/01/2013 06:30 PM, Katie Bettencourt wrote:

Ok, I understand that, except that all of my runs are like that, but only a few of them errored out. Why is that?

Katie

On Fri, Mar 1, 2013 at 3:38 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Hi Katie, the problem is that eventtypes 1 and 2 are synchronized
32 sec apart. What this means is that they are effectively one
event if you set the time window longer than 32 sec (you have it
set to 34). There is no way around this. If you want a longer
window, use 30 sec (32 might work).
doug

On 02/28/2013 04:46 PM, Katie Bettencourt wrote:

    Here it is for one of the failed runs.  Let me know if you
    need anything else.

    Katie

    On Thu, Feb 28, 2013 at 3:27 PM, Douglas N Greve
    <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>> wrote:

        Can you send me the Xtmp.mat file from the outputdirectory?
        doug

        On 02/28/2013 07:34 AM, Katie Bettencourt wrote:

            Still looking for an answer why my analysis gives me
    an ill
            conditioned error.  I have run this analysis fine
    before, with
            a timewindow of 22,  but when I tried to change the time
            window to 34, selxavg3-sess gives me an ill
    conditioned error
            on some of the runs (each run is being analyzed
    separately),
            but not all of them.  All the runs are identical
    except for
            the order the conditions appear in, but each condition
    appears
            an equal number of times and for an equal duration in each
            run.  There is nothing specific about the runs that
    fail or
            the subjects that they fail in (for some subjects all
    8 runs
            work fine, others lost between 1-3 runs to this
    error).   I'm
            doing svm with this data so I need all conditions to be
            analyzed correctly.

            Any help?

            Katie

            On Mon, Feb 25, 2013 at 10:23 AM, Katie Bettencourt
            <kcb@wjh.harvard.edu <mailto:kcb@wjh.harvard.edu>
    <mailto:kcb@wjh.harvard.edu <mailto:kcb@wjh.harvard.edu>>
            <mailto:kcb@wjh.harvard.edu
    <mailto:kcb@wjh.harvard.edu> <mailto:kcb@wjh.harvard.edu
    <mailto:kcb@wjh.harvard.edu>>>> wrote:

                No, each condition has at least 3 instances of it
    in each run.
                 The runs are all set up exactly the same, just
    the order
            changes,
                so there is nothing different about the runs that work
            than the
                runs that fail, and again, all of these runs
    worked fine
            with the
                exact same paradigm files and set up, but only the
            timewindow at
                22 instead of 34.

                Katie


                On Mon, Feb 25, 2013 at 10:21 AM, Douglas N Greve
                <greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
            <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
            <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>

            <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:

                    Hi katie, I'm guessing that you have one event
    type
            that only
                    has one event? If so, you can do what Sebastian
            suggests, but
                    you won't be able to look at contrasts related
    to that
            condition.
                    doug



                    On 02/19/2013 03:24 PM, 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


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

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