Hi, I got an error when running recon-all -stage3.I've included the relevant part of the log below. Any ideas as to what went wrong? Thanks, alex
writing spherical brain to /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere spherical transformation took 0.91 hours navgs=32 and tol=1.000e-01 integrating with navgs=32 and tol=1.000e-01 integrating with navgs=8 and tol=1.000e-01 taking momentum steps... integrating with navgs=8 and tol=1.000e-01 integrating with navgs=8 and tol=1.000e-01 integrating with navgs=2 and tol=1.000e-01 taking momentum steps... integrating with navgs=2 and tol=1.000e-01 integrating with navgs=2 and tol=1.000e-01 integrating with navgs=0 and tol=1.000e-01 pass 1 complete, delta sse/iter = 0.16/60 = 0.00 final distance error %31.34 optimization complete. unfolding took 0.81 hours --------------------------------------------- Fix Topology lh Sat Jun 11 04:24:54 EST 2005 /data/flanders/work/alex/freesurfer/subjects/1000192/scripts mris_fix_topology 1000192 lh reading input surface /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere... before topology correction, eno=-301 (nv=188932, nf=378516, ne=567749, g=151) mrisReadTriangleFile(/data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.orig): surface doesn't match /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere
No such file or directory mrisReadTriangleFile failed.
No such file or directory MRISreadOriginalProperties: could not read surface file orig No such file or directory mris_fix_topology: could not read original surface orig No such file or directory reading T1 volume from T1... reading wm segmentation from wm...
recon-all exited with errors at Sat Jun 11 04:24:58 EST 2005
Hi Alex,
that's a starnge one. Did the partition run out of space? Can you do an ls -l in the surf dir and send it along? Also, run mris_euler_number on lh.orig, lh.smoothwm, lh.inflated and lh.qsphere.
On Tue, 14 Jun 2005, Fornito, Alexander wrote:
Hi, I got an error when running recon-all -stage3.I've included the relevant part of the log below. Any ideas as to what went wrong? Thanks, alex
writing spherical brain to /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere spherical transformation took 0.91 hours navgs=32 and tol=1.000e-01 integrating with navgs=32 and tol=1.000e-01 integrating with navgs=8 and tol=1.000e-01 taking momentum steps... integrating with navgs=8 and tol=1.000e-01 integrating with navgs=8 and tol=1.000e-01 integrating with navgs=2 and tol=1.000e-01 taking momentum steps... integrating with navgs=2 and tol=1.000e-01 integrating with navgs=2 and tol=1.000e-01 integrating with navgs=0 and tol=1.000e-01 pass 1 complete, delta sse/iter = 0.16/60 = 0.00 final distance error %31.34 optimization complete. unfolding took 0.81 hours
Fix Topology lh Sat Jun 11 04:24:54 EST 2005 /data/flanders/work/alex/freesurfer/subjects/1000192/scripts mris_fix_topology 1000192 lh reading input surface /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere... before topology correction, eno=-301 (nv=188932, nf=378516, ne=567749, g=151) mrisReadTriangleFile(/data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.orig): surface doesn't match /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere
No such file or directory mrisReadTriangleFile failed.
No such file or directory MRISreadOriginalProperties: could not read surface file orig No such file or directory mris_fix_topology: could not read original surface orig No such file or directory reading T1 volume from T1... reading wm segmentation from wm...
recon-all exited with errors at Sat Jun 11 04:24:58 EST 2005
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Fornito, Alexander