Hi Bruce,
Thanks! The lh.orig.nofix surface follows the white matter perfectly,
but the lh.orig surface does not. So I suspect that the topology fixing
step is creating this problem.
However, when I load lh.defect_labels this area is not marked as a
defect, nor are there any major defects labeled nearby (see
http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/lh_wm_defect.tif for
image). Does this mean that the topology fixing is not editing this area?
If it is the topology fixing, are there parameters of mris_fix_topology,
mris_euler_number or mris_remove_intersection that I can alter in order
to fix this problem, without wreaking havoc in other areas? Or any
other suggestions would be much appreciated!
Best,
Katie
Bruce Fischl wrote:
Hi Katie,
try looking at the lh.orig.nofix and lh.inflated.nofix surfaces to see
if you can see the defect.
cheers,
Bruce
On Thu, 23 Apr 2009, Kathryn Devaney wrote:
Hi Bruce & surfers,
That's what I thought initially, but then I did edit the wm.mgz to
remove topological defects, and re-ran the reconstruction from the
'fill' step, and this problem remains. I can't find a nearby defect
in the wm.mgz volume to edit, but maybe there is something that isn't
obvious to me.
I put up coronal, axial, and sagittal views of the problem area &
neighborhood up at:
http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/coronal_wm_defect.tif
http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/horizontal_wm_defect.tif
http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/sagittal_wm_defect.tif
Maybe there is a defect around this area which I'm not seeing?
Otherwise, is there something else that I can do? Also, let me know
if you'd like to check out the data, and I can put it somewhere
accessible.
Thanks!
Katie
Bruce Fischl wrote:
Hi Katie,
looks like an incorrectly fixed topological defect. You need to edit
the wm.mgz to remove the defect and rerun autorecon2-wm
cheers,
Bruce
On Wed, 22 Apr 2009, Kathryn Devaney wrote:
Hello freesurfers,
I am running a reconstruction of a macaque in stabe4, and I am
having a
problem with the smooth white matter surface not following the wm
boundary
in the wm.mgz volume (please see attached for examples in the wm
and T1
volumes).
The non-wm area included in the surface was never part of the wm
volume,
but I edited the other defects in wm.mgz and re-ran fill, tessellate,
smooth1, inflate1, qsphere, fix, finalsurfs, smooth2, amd inflate2.
Unsurprisingly, this problem persisted.
Is there anything that I can do to fix this?
Thanks!
Katie
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