Hi Eric,

Have you tried to manually set the cutting planes?

Jenni

On Mon, 29 Aug 2005, Yuan-Fen Kuo wrote:

Hi.

I am ( again) trying out the stage1 work flow. I have been encountering the following error during the fill step which terminates the work flow.

mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst ERROR: mri_fill exited with non-zero status recon-all exited with errors at Mon Aug 29 14:02:23 CDT 2005

how may I go about solving this?

The complete output is at the end of the message.

Thank you for help, Eric

Yuan-Fen Kuo Associate Imaging Processing Specialist Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison

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Fill Mon Aug 29 14:01:26 CDT 2005 INFO: Uses mri/transforms/talairach.xfm mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm wm filled /Users/Shared/freesurfer/subjects/005CO/mri logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Volume /tmp/mritotal_20452/nu_8_dxyz.mnc cannot be found. INFO: Using transforms/talairach.xfm and its offset for Talairach volume ... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.078 -0.013 -0.035 -5.822; 0.018 1.076 0.141 -29.222; 0.032 -0.136 1.035 16.018; 0.000 0.000 0.000 1.000; mri_fill: could not find valid seed for the cc No such file or directory Looking for area (min, max) = (350, 1400) area[0] = 12102 (min = 350, max = 1400), aspect = 0.79 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... Looking for area (min, max) = (350, 1400) area[0] = 12102 (min = 350, max = 1400), aspect = 0.79 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst ERROR: mri_fill exited with non-zero status recon-all exited with errors at Mon Aug 29 14:02:23 CDT 2005 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer