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 > <[email protected] <mailto:[email protected]>> 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 > <[email protected] <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>>> 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 > <[email protected] <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>> > <mailto:[email protected] > <mailto:[email protected]> <mailto:[email protected] > <mailto:[email protected]>>>> 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 > <[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > <mailto:[email protected] > <mailto:[email protected]> > > <mailto:[email protected] > <mailto:[email protected]>>>> 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 > [email protected] <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > <mailto:[email protected] > <mailto:[email protected]> > > <mailto:[email protected] > <mailto:[email protected]>>> > > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > 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. > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] <mailto:[email protected]> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
