You said initially that you were using FS v5.1, but that recon- all.local-copy is not consistent with FS v5.1.
Are you processing subjects from scratch? If so, then you need to check your path/environment and figure out why an older version of recon-all is being called when you think that you're using v5.1. Please cc the list on communication so that the thread is captured in the FS archives for others benefit. cheers, -MH On Fri, 2011-12-30 at 16:52 +0000, LAOUCHEDI MAKHLOUF wrote: > hi michael > in fact i gedited the recon-all.local-copy in > <subjdir>/scripts and i noticed that the section "Cortical > Parcellation 2 " contains references to a2005s and not to a2009s. is > it a good idea to replace a2005s by a2009s in the text, then make a > copy of the file and put it somewhere (my current directory for > example) and then use it instead of the one given in > <FREESURFER_HOME>/bin ?. then should i do the same modifications in > the other parts of the text (for example the section "AParc2ASeg " and > "Surface Anatomical Stats 2" ...) ?. > i attached the recon-all.local-copy > file. > > thanks for all > > --- En date de : Ven 30.12.11, 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: Vendredi 30 décembre 2011, 16h57 > > > 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
