Hi Bruce, I ran the topology fixer again and it seemed to work. Unfortunately, silly me just wrote over the original files, so all I have is the euler number from the orig surface that is output in the recon-all log.
Euler Number lh Sat Jun 11 04:20:04 EST 2005 /data/flanders/work/alex/freesurfer/subjects/1000192 mris_euler_number /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.orig euler # = v-e+f = 2g-2: 179761 - 539277 + 359518 = 2 --> 0 holes F =2V-4: 359518 = 359522-4 (0) 2E=3F: 1078554 = 1078554 (0)
total defect index = 0 Euler: NHoles = 0
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 6/14/2005 10:12 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all stage3 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
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then you should just run the rest of the analysis I guess and see if it works. In general all the surfaces of a hemisphere should have the same # of edges/faces/vertices *except* the ?h.qsphere surface. They should have all have an euler number of 2.
cheers, Bruce
On Wed, 15 Jun 2005, Fornito, Alexander wrote:
Hi Bruce, I ran the topology fixer again and it seemed to work. Unfortunately, silly me just wrote over the original files, so all I have is the euler number from the orig surface that is output in the recon-all log.
Euler Number lh Sat Jun 11 04:20:04 EST 2005 /data/flanders/work/alex/freesurfer/subjects/1000192 mris_euler_number /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.orig euler # = v-e+f = 2g-2: 179761 - 539277 + 359518 = 2 --> 0 holes F =2V-4: 359518 = 359522-4 (0) 2E=3F: 1078554 = 1078554 (0)
total defect index = 0 Euler: NHoles = 0
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 6/14/2005 10:12 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all stage3 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
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Fornito, Alexander