Check the skull strip. Sometimes this happens when some structure is not
removed. Also check whether the brain stem and cerebellum have been
properly cut away and that the hemispheres have been properly separated
(look at the wm.mgz for this).
David Qixiang Chen wrote:
> Hi,
> We are having one
where is it getting stuck? that is, look at the recon-all.log (and
recon-all.cmd file). often times recon-all gets stuck in the topology
fixer, because of some horrible wm.mgz file, which itself could be due
to other problems. also, i assume the first thing performed before
starting recon-all was
Hi David,
usually this means the topology fixing has encountered a very large
defect, typically caused by the cerebellum or skull being attached to one
of the cortical hemispheres. Try looking at the orig.nofix in tksurfer or
the filled.mgz in tkmedit and do a sanity check on them.
cheers,
Bru
Hi,
We are having one scan going through recon-all that is taking way
longer than ordinary. Other scans took about 20-30 hours to calculate,
while this particular scan is taking 3+ days and has still not being
completed.
Just wondering how often something like this happens, and if there's
any known
