Hi Nick, hi everyone,
I just ran the 3.0.2 topology fixer on a linux machine over one of the
failed surfaces, and that seems to have worked - great! The compute
servers have since been upgraded to 3.0.3, so I'll feed the results into
the rest of the recon-all pipeline and see how it goes.
Thanks for all your help,
Johannes
Nick Schmansky schrieb:
Johannes,
In looking at your recon-all.log, it looks like you are running v3.0.1
of freesurfer, which can be confirmed by typing:
cat $FREESURFER_HOME/build-stamp.txt
In v3.0.2, a bug in the topology fixer was fixed (namely, the
'mrisDefectAnalysis' routine).
Is it possible for you to download the latest freesurfer and rerun on
the trouble subjects? It should not be necessary to re-run on the other
subjects. The fixed topology fixer is likely to successfully process
your subjects.
I can also send you this new mris_topology_fixer binary for the Mac if
you don't want to download/re-install.
Nick
On Wed, 2006-07-12 at 18:50 +0100, Johannes Klein wrote:
Hi Nick,
Thanks for your message. Unfortunately, the topology fixer did not
produce a defect_labels file, it seems to have aborted before doing so.
Is there a way to make mris_fix_topology produce the defect labels
without actually running topology correction? I thought of trying the
-correct_defect option with one of the defects that didn't cause
problems. Does that make sense?
Thanks,
Johannes
Nick Schmansky schrieb:
Johannes,
To visualize defect locations:
tksurfer <subjid> lh inflated.nofix
then:
File->Curvature->Load Curvature
select:
surf/lh.defect_labels
and the defects will display in red.
Remember you can click on a defect vertex in tksurfer, then click 'save
point' and then in tkmedit, click 'goto saved point', which is handy to
see exactly where in a volume things went wrong.
Nick
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