Anne

>>> Bruce Fischl <fischl@nmr.mgh.harvard.edu> 24/10/2012 13:42 >>>
Hi Anne

can you cc the list so others can answer? What version are you running?
This is something we fixed a while ago

cheers
Bruce

On Wed, 24 Oct 2012, Anne Uhlmann
wrote:

> Hi Bruce,
>
> Sorry about that. Please find the recon-all.log file attached. The error
> message given there is: ERROR: _FindFacePath: could not find path!
>
> No rh output is getting produced.
> When viewing the brainmask.mgz -surfs, an error message says: rh.white:
> could not open file.
>
> When trying to view rh.orig.nofix, the error message says: rh.pial: no such
> file or directory. But the wm outline looks just like the lh one, very
> angular but otherwise no defects. Sometimes voxels are included that should
> not be white matter and in the occipital area some of the white matter is
> excluded.
>
> I can't say much about the rh.inflated.nofix. I can only view it in tkmedit
> and it seems to have some fine disruptions in the occipital area.
>
> Thanks for your help.
> Regards, Anne
>
>
>
>
> >>> Bruce Fischl <fischl@nmr.mgh.harvard.edu> 22/10/2012 15:50 >>>
> Hi Anne
>
> can you post the whole recon-all.log file? I don't think you included the
> actual error message. Also, you can look at the rh.inflated.nofix and
> rh.orig.nofix to see if there are any really big defects in the rh before
> fixing. Is no rh output produced?
>
> Bruce
>
> On Mon, 22 Oct 2012, Anne Uhlmann wrote:
>
> > Hi there,
> >
> > I am having trouble with one of my scans where the right hemisphere is not
> > getting included in the analysis from the "Fix Topology rh" point on. This
> > is the error message I get:
> >
> > Linux cnode-2-52 2.6.18-308.el5 #1 SMP Tue Feb 21 20:06:06 EST 2012 x86_64
> > x86_64 x86_64 GNU/Linux
> > $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $
> > /SCRATCH4/cubic/auhlmann/freesurfer/bin/recon-all
> >PWD/lustre/SCRATCH4/cubic/auhlmann/freesurfer/subjects/meth_output_test3/MA
> S11
> > 2.12.1107.5.2/scripts
> > CMD mris_topo_fixer -mgz -warnings -seed 1234 MAS112.12.1107.5.2 rh
> >
> > The orig.mgz looks OKish (it's not great) except for some kind of a
> scanner
> > artifact in 2 slices of the scan. I tried to fix it with control points
> and
> > making edits to the white matter, but unfortunately it didn't solve the
> > problem. I am grateful for any suggestions.
> >
> > Thank you and best regards,
> > Anne
> >
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