This data was processed with FSv4.0.2, then edited, we upgraded to the latest v4.0.4 and now I am trying to run recon-all with the -autorecon2-cp flag.

I'll try your work around on one of the subjects.
Is the aseg.auto_noCCseg.mgz volume usually the same as the aseg.auto.mgz volume? And does this mean that we will lose the CorpusCallosum segmentation for these subjects?


At 04:44 PM 5/29/2008, 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

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