For some reason the beginning section of the recon-all.log that you sent is missing (i.e,. the part containing the actual command that you ran). What was the exact recon-all command that you used? From the log file, only the very first mri_convert was performed. Was your command perhaps recon-all -i <input.nii> -s <subjname>
If so, you need to include the -all flag to actually run all the rest of the recon-all stream. cheers, -MH On Fri, 2011-12-30 at 13:55 +0000, LAOUCHEDI MAKHLOUF wrote: > Hi Michael > i looked in and the file doesn't contain a section > called "Cortical Parc 2" . what do you think is the problem ? i > attached the log > > thanks > > > > --- En date de : Jeu 29.12.11, Michael Harms <mha...@conte.wustl.edu> > a écrit : > > De: Michael Harms <mha...@conte.wustl.edu> > Objet: Re: [Freesurfer] aparc.a2009s+aseg problem > À: "LAOUCHEDI MAKHLOUF" <laouma...@yahoo.fr> > Cc: freesurfer@nmr.mgh.harvard.edu > Date: Jeudi 29 décembre 2011, 18h17 > > > That is a job log from your cluster, which isn't helpful to > the issue at > hand. > > You need to look in <subjdir>/scripts/recon-all.log, which > contains a > complete log of the entire recon-all processing stream. > > cheers, > -MH > > On Thu, 2011-12-29 at 17:10 +0000, LAOUCHEDI MAKHLOUF wrote: > > Hi Michael > > i looked in the job.log file (i am using a > condor > > cluster) that i attached, and there is no such section! > > > > thanks > > > > --- En date de : Jeu 29.12.11, Michael Harms > <mha...@conte.wustl.edu> > > a écrit : > > > > De: Michael Harms <mha...@conte.wustl.edu> > > Objet: Re: [Freesurfer] aparc.a2009s+aseg problem > > À: "LAOUCHEDI MAKHLOUF" <laouma...@yahoo.fr> > > Cc: freesurfer@nmr.mgh.harvard.edu > > Date: Jeudi 29 décembre 2011, 18h01 > > > > > > The problem is apparently that the > Xh.aparc.a2009s.annot > > wasn't created. > > > > Look in scripts/recon-all.log and make sure that the > section > > "Cortical > > Parc 2" is present, and if it is, look for clues as > to why > > the .annot > > wasn't created. > > > > cheers, > > -MH > > > > On Thu, 2011-12-29 at 16:03 +0000, LAOUCHEDI > MAKHLOUF wrote: > > > hi everyone > > > i run recon-all on 27 subjects > using the > > 5.1 > > > version, and i don't find aparc.a2009s+aseg.mgz > neither > > > lh.aparc.a2009s.annot so i can't use the command > > mri_aparc2aseg > > > ( mri_aparc2aseg --s subject --a2009s). what must > i do to > > have > > > aparc.a2009s+aseg.mgz. > > > > > > thanks > > > > > > _______________________________________________ > > > 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. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
