Hi Bruce,

Just to let you know the new mris_topo_fixer worked and there was no error with the recon. 

I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples..

Cheers,
Hugh


On 16 November 2012 14:44, Hugh Pemberton <hughpemberton1@gmail.com> wrote:
Hi Bruce,

I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a few screen shots as examples..

Cheers,
Hugh


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/BugReporting

Many thanks in advance,
Best,
Hugh

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