Looks like it tried both -
mris_fix_topology failed! (euler number != 2) Trying mris_topo_fixer...
cp ../surf/lh.orig.nofix ../surf/lh.orig
euler # = v-e+f = 2g-2: 144765 - 434289 + 289525 = 1 --> 1 holes F =2V-4: 289525 != 289530-4 (1) 2E=3F: 868578 != 868575 (3)
total defect index = 4
cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere
cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm
/home/hughp/freesurfer/subjects/B______________________/scripts
mris_topo_fixer -mgz -warnings -seed 1234 B_____________________ lh
On 16 November 2012 11:14, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
this is a bug in the topology fixer. Maybe Zeke or Nick can post a new version of it? Was it mris_topo_fixer that was runing or mris_fix_topology?
On Fri, 16 Nov 2012, Hugh Pemberton wrote:
Hi Bruce,
Thanks for getting back to me. In terminal window it says "freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0" but recon-all -version give me "$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $"
Hugh
On 16 November 2012 11:05, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Hugh This is fixed in the newest version. What version are you running? Bruce
On Nov 15, 2012, at 6:48 PM, Hugh Pemberton hughpemberton1@gmail.com wrote:
Hi,I have just received this error after a recon-all subjid- ___ all :
ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/**subjects/B______________/**scripts
mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig
rm ../surf/lh.inflated
cp ../surf/lh.orig_corrected ../surf/lh.orig
Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s B______________ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012
To report a problem, see http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Many thanks in advance, Best, Hugh
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