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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > <k...@wjh.harvard.edu <mailto:k...@wjh.harvard.edu> > <mailto:k...@wjh.harvard.edu <mailto:k...@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 > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > 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/ > > > > > 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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > 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 gr...@nmr.mgh.harvard.edu 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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
