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/MAS112.12.1107.5.2/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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UNIVERSITY OF CAPE TOWN
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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/MAS11 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
###
UNIVERSITY OF CAPE TOWN
This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity.
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freesurfer@nmr.mgh.harvard.edu
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Anne Uhlmann -
Bruce Fischl