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:[EMAIL PROTECTED]
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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