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