the new mris_topo_fixer is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/
On Wed, 2012-10-24 at 09:22 -0400, Bruce Fischl wrote:
yes, that should be fine.
On Wed, 24 Oct 2012, Anne Uhlmann wrote:
OK, thank you. That would be great. Can I just run the new topo_fixer within my old freesurfer version?
Cheers, Anne
Bruce Fischl fischl@nmr.mgh.harvard.edu 24/10/2012 15:15 >>>
Hi Anne
you should grab a new version of mris_topo_fixer. Nick or Zeke can post it for you. The problem may be related to your artifact, but the new one will at least complete and produce surfaces, although they may not be accurate and you might have to do some editing.
cheers Bruce
On Wed, 24 Oct 2012, Anne Uhlmann wrote:
Hi Bruce,
I am running freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 on a
cluster
(which I access via putty). It's the only scan that has some kind of a scanner artifact and that shows this particular problem, therefore I thought there might be a link.
Thanks, 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/
M
A
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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