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 <fis...@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 <fis...@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 <hughpembert...@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/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>
>> Many thanks in advance,
>> Best,
>> Hugh
>>
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