Re: [Freesurfer] ERROR: cannot find .../mri/aseg.auto_noCCseg.mgz

the cc gets put into the aseg.auto.mgz I think to create the aseg.auto_CC.mgz or something like that. Nick: is that right?

On Thu, 29 May 2008, Sky Raptentsetsang wrote:

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