Sky,

The best option for you is to, is Bruce suggests:

cp aseg.auto.mgz aseg.auto_noCCseg.mgz

Nick

On Thu, 2008-05-29 at 19:44 -0400, Bruce Fischl wrote:
> and what version are you running? The easiest thing to do would be to
> cp aseg.auto.mgz aseg.auto_noCCseg.mgz
>
> then try again. I think Nick fixed this in the current version
> On
> Thu, 29 May 2008, Sky Raptentsetsang wrote:
>
> > Hi Bruce,
> > I have the following of the specified files in the ../mri dir:
> > aseg.auto.mgz
> > aseg.auto_CCseg.mgz
> > aseg.mgz
> >
> >
> > Sky
> >
> > At 04:00 PM 5/29/2008, Bruce Fischl wrote:
> >       can you see what aseg*.mgz volumes there are in your mri dir?
> >       On Thu, 29 May 2008, Sky Raptentsetsang wrote:
> >
> >             Hello,
> >             I am re-running edited data through
> >             -autorecon2-cp and during the
> >             mri_fill script I receive the following error
> >             message:
> >             #@# Fill Tue May 27 09:44:29 PDT 2008
> >             /cind/00/PCDv4/Freesurfer/subjects/P018-1/mri
> >              mri_fill -a ../scripts/ponscc.cut.log -xform
> >             transforms/talairach.lta
> >             -segmentation aseg.auto_noCCseg.mgz wm.mgz
> >             filled.mgz
> >             logging cutting plane coordinates to
> >             ../scripts/ponscc.cut.log...
> >             INFO: Using transforms/talairach.lta and its
> >             offset for Talairach volume
> >             ...
> >             using segmentation aseg.auto_noCCseg.mgz...
> >             reading input volume...done.
> >             searching for cutting planes...voxel to talairach
> >             voxel transform
> >              0.956  -0.049   0.061  -5.626;
> >              0.029   1.045   0.352  -16.780;
> >             -0.078  -0.277   0.950   31.426;
> >              0.000   0.000   0.000   1.000;
> >             mri_fill: could not read segmentation from
> >             aseg.auto_noCCseg.mgz
> >             reading segmented volume aseg.auto_noCCseg.mgz...
> >             ERROR: cannot find
> >             /cind/00/PCDv4/Freesurfer/subjects/P018-1/mri/aseg.auto_noCCseg.mgz
> >             No such file or directory
> >             Linux polaris.v21.med.va.gov 2.6.20-1.2307.fc5 #1
> >             SMP Sun Mar 18 20:58:09
> >             EDT 2007 x86_64 x86_64 x86_64 GNU/Linux
> >             recon-all exited with ERRORS at Tue May 27
> >             09:44:34 PDT 2008
> >
> >             In this directory there is a aseg.auto_CCseg.mgz
> >             file, but no
> >             aseg.auto_noCCseg.mgz file.
> >             This data was originally processed with FSv4.0.2
> >             and then edited and we
> >             upgraded to the latest v4.0.4.
> >             Can anyone tell me what the difference between
> >             the *_CCseg.mgz and
> >             *_noCCseg.mgz file is? and how I can proceed?
> >
> >             Thanks in advance for any help!
> >
> >             Sky Raptentsetsang
> >             Staff Research Associate
> >             CIND, San Francisco VAMC
> >             Department of Radiology, UCSF
> >             4150 Clement St. Bldg. 13, 2nd Floor, Mail Stop
> >             114M
> >             San Francisco, CA 94121
> >             Phone 415.221.4810 ext. 4186
> >             Fax 415.386.3954
> >
> >       Sky Raptentsetsang
> >
> >       Staff Research Associate
> >       CIND, San Francisco VAMC
> >       Department of Radiology, UCSF
> >       4150 Clement St. Bldg. 13, 2nd Floor, Mail Stop 114M
> >       San Francisco, CA 94121
> >       Phone 415.221.4810 ext. 4186
> >       Fax 415.386.3954
> >
> >
> >
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