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 mharms@conte.wustl.edu a écrit :

    De: Michael Harms <mharms@conte.wustl.edu>
    Objet: Re: [Freesurfer] aparc.a2009s+aseg problem
    À: "LAOUCHEDI MAKHLOUF" <laoumakhl@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
    <mharms@conte.wustl.edu>
    > a écrit :
    >         
    >         De: Michael Harms <mharms@conte.wustl.edu>
    >         Objet: Re: [Freesurfer] aparc.a2009s+aseg problem
    >         À: "LAOUCHEDI MAKHLOUF" <laoumakhl@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
    >         > 
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