Try re-running recon-all -qcache for that subject and see if the error goes away
On 05/11/2016 10:56 AM, Marissa Pifer wrote: > The error was generated on that first subject 03-1, but it was > successful on all of the other subjects. Is there something wrong with > that file that we have to exclude that subject from the analysis? > > Marissa > > On Wed, May 11, 2016 at 10:38 AM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > OK, it is failing on the mri_concat command. It may be that one > of those inputs is causing the problem. Can you run the command > with each input separately, eg, > mri_concat > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-1.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh > --o deleteme.mgh > mri_concat > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-2.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh > --o deleteme.mgh > ... > > and see if there is one that generates the error > > > > On 5/11/16 9:15 AM, Marissa Pifer wrote: >> Here is everything in the terminal after I hit analyze: >> >> Data table loading completed successfully. >> >> SUBJECTS_DIR is '/Users/marchaut/Documents/myprojects/SOARmaster' >> >> lh-Avg-Intercept-thickness ----------------------- >> >> Does the average thickness differ from zero? >> >> 1.000 1.000; >> >> >> lh-Diff-1-2-Intercept-thickness ----------------------- >> >> Does the average thickness differ between 1 and 2? >> >> 1.000 -1.000; >> >> >> ninputs = 28 >> >> Checking inputs >> >> mri_concat(4256,0x7fff78a00310) malloc: *** >> mach_vm_map(size=4619122851646017536) failed (error code=3) >> >> *** error: can't allocate region >> >> *** set a breakpoint in malloc_error_break to debug >> >> znzTAGskip: tag=586130367, failed to calloc 2856323072 bytes! >> >> >> Cannot allocate memory >> >> Error in Analyze: command failed: mri_concat >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-1.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-2.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR04-1.long.SOAR04/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR04-2.long.SOAR04/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR05-1.long.SOAR05/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR05-2.long.SOAR05/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR06-1.long.SOAR06/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR06-2.long.SOAR06/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR07-1.long.SOAR07/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR07-2.long.SOAR07/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR09-1.long.SOAR09/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR09-2.long.SOAR09/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR17-1.long.SOAR17/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR17-2.long.SOAR17/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR19-1.long.SOAR19/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR19-2.long.SOAR19/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR23-1.long.SOAR23/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR23-2.long.SOAR23/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1.long.SOAR26/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-2.long.SOAR26/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR27-1.long.SOAR27/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR27-2.long.SOAR27/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR28-1.long.SOAR28/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR28-2.long.SOAR28/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR30-1.long.SOAR30/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR30-2.long.SOAR30/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR31-1.long.SOAR31/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR31-2.long.SOAR31/surf/lh.thickness.fwhm10.fsaverage.mgh >> --o /Users/marchaut/Documents/myprojects/SOARmaster/qdec/test1/y.mgh >> >> XIO: fatal IO error 35 (Resource temporarily unavailable) on X >> server "/tmp/launch-NzfFao/org.macosforge.xquartz:0" >> >> after 16398 requests (16398 known processed) with 0 events >> remaining. >> >> >> On Tue, May 10, 2016 at 5:41 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> Is that all it says? At one point (about 3-4 years ago) we >> would see >> that error because some of our files got corrupted. Can you >> send more of >> the terminal output? >> >> On 05/10/2016 12:56 PM, Marissa Pifer wrote: >> > Hi freesurfers, >> > >> > I am on a macbook pro OSX 10.9.5, trying to run an analysis >> on qdec - >> > freesurfer version 5.3. I am looking to analyze T2weighted >> scans for >> > 27 subjects through the qdec system. I keep getting this >> error that it >> > cannot allocate memory for the task. I'v been talking with >> our IT >> > people and they've told me I have more than enough space on the >> > computer, so it must be an issue with the program or how >> it's set up. >> > >> > This is the error message: >> > >> > >> > *** error: can't allocate region >> > >> > *** set a breakpoint in malloc_error_break to debug >> > >> > znzTAGskip: tag=586130367, failed to calloc 2856323072 bytes! >> > >> > >> > Cannot allocate memory >> > >> > >> > >> > Does anyone know what I can do to fix this problem? >> > >> > Thanks, >> > >> > Marissa >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> 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/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto: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. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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
