No. At least for this particular subject, when I run recon-all it does not create the noCCseg file. However, I have only been starting from autorecon2. Does this make a difference? Also, I have just downloaded version 4.2...if I run it using the new version will it create the files I need? Also, I have a subject who outputs this error:
mris_make_surfaces: could not read segmentation volume /misc/data14/jen/FreesurferTest/JPP_111/surface_2/mri/aseg.mgz This subject DOES have the noCCseg file. I've sent the recon-all.log files to Nick Schmansky, maybe that will shed some light on the issue. -----Original Message----- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Mon 2/16/2009 3:33 PM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] still exiting with errors the current versions should have aseg.auto_noCCseg.mgz. When you rerun recon-all doesn't it create them? On Sun, 15 Feb 2009, Dankner, Nathan (NIH/NIMH) [F] wrote: > The aseg files in mri are aseg.auto.mgz and aseg.auto_CCseg.mgz. The scans that are working seem to have aseg.auto_noCCseg.mgz instead of CCseg.mgz. > > > -----Original Message----- > From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > Sent: Fri 2/13/2009 8:44 PM > To: Dankner, Nathan (NIH/NIMH) [F] > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] still exiting with errors > > what files are in [subject path]/mri/*aseg*.mgz? > > On Fri, 13 Feb 2009, Dankner, Nathan (NIH/NIMH) [F] wrote: > >> Sorry to post this again, but I am still having issues with surfaces exiting >> with errors. These are the two outputs that I have gotten: >> >> MRI_fill: could not read segmentation from aseg.auto_noCC.mgz >> reading segmented volume aseg.auto_noCCseg.mgz... >> ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz >> No such file or directory >> >> and >> >> ERROR: cannot find [subject path]/mri/aseg.mgz >> >> Mr. Schmansky indicated that this may be due to 2 different versions being >> used. I have been running recon-all on version 4.1.0 on a 64 bit linux >> machine, and editing on the same version but on a mac. Also, I attempted to >> use the -clean-aseg command as directed, but this doesn't seem to have fixed >> the problem. I'm currently in the process of updating both machines to >> version 4.2.0, so I don't know how this will affect things. Any >> suggestions? Thanks in advance, >> >> Nathan >> >> _______________________________________________ >> 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
