1 Nov
2012
1 Nov
'12
2:38 p.m.
how much ram do you have? On Thu, 1 Nov 2012, Christine Smith wrote:
Well, that is funny. Now it has finished without errors. I am not quite sure what happened. The command line was the same both times: recon-all -make all -subjid CON1
Is it possible that some other process that was going on on our server caused the processing for this subject to end abnormally? We sometimes run 3 subjects at a time, but this does not exhaust our RAM or the number of processors.
Christine
On Wed, Oct 31, 2012 at 9:31 AM, Christine Smith cnsmith@ucsd.edu wrote: The command line was: recon-all -make -s CON1
I am not sure why the log said it was: recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel I am running it again right now and it said the command line was: recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -careg -careginv It seems to be running through the processing stream. I will let you know what it says after it finishes sometime tomorrow. Christine On Tue, Oct 30, 2012 at 6:13 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > so your recon-all command line was: > > recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel > > usually -s just takes the subject name/identifier, not the whole path, and > why are you only rerunning calabel? I don't see what the error is, but this > is an unusual usage > > > > > On Tue, 30 Oct 2012, Christine Smith wrote: > >> See my original post at the end of this message and some more >> information included below. >> >> What would have been edited between the previous run without errors >> and the current run with errors is the brainmask, the wm.mgz file, and >> control points. >> >> On Tue, Oct 30, 2012 at 1:21 PM, Christine Smith <cnsmith@ucsd.edu> wrote: >>> >>> Here it is: >>> >>> New invocation of recon-all >>> >>> Thu Oct 4 03:52:22 PDT 2012 >>> /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 >>> /usr/local/freesurfer/bin/recon-all >>> -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel >>> #-------------------------------------- >>> #@# SubCort Seg Thu Oct 4 03:52:22 PDT 2012 >>> >>> mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff >>> aseg.manedit.mgz >>> >>> Linux squirelab.ucsd.edu 2.6.18-308.13.1.el5 #1 SMP Tue Aug 21 >>> 18:44:22 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux >>> >>> recon-all -s CON1 exited with ERRORS at Thu Oct 4 03:52:22 PDT 2012 >>> >>> On Tue, Oct 30, 2012 at 12:45 PM, Bruce Fischl >>> <fischl@nmr.mgh.harvard.edu> wrote: >>>> >>>> what were the last 20 lines or so of the recon-all.log? >>>> >>>> On Tue, 30 Oct 2012, Christine Smith wrote: >>>> >>>>> Hello, >>>>> >>>>> After successfully running a subject through freesurfer (recon-all >>>>> -make all) several times as I fixed some pial and white matter edits, >>>>> I now get the message that recon-all finished with errors. Inspection >>>>> of the recon-all.log doesn't reveal any error messages to me in any >>>>> particular step. >>>>> >>>>> What should I be looking for to track down the reason that errors were >>>>> generated? >>>>> >>>>> I already examined the talairach transform and that looks great. >>>>> I loaded the pial and white matter surfaces and they look fine. The >>>>> segmentation aparc+aseg looks great too. >>>>> >>>>> Thanks, >>>>> Christine >>>>> >>>>> >>>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > 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. >-- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego
-- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego