Hi Trinh
why is that a problem? The post-fixing surfaces (pial, white, inflated,
etc...) are supposed to have 0 holes/handles. In the tutorial it is not
that the topo fixer doesn't give the right topology - it always does.
Rather, the correction of the topology causes an incorrect geometry that
you need to fix.
cheers
Bruce
On Fri, 9 Oct 2015, Thục Trinh
wrote:
Hi Bruce,
I am still confusing about my subjects'recon that I still doubt my skill on
detecting the topological error. Therefore, I practice on the FStutorial
data and run the mris_euler_number on the "topo_defect_before" to see what
happens. The result returns me with 0 holes for all ?h.pial, ?h.white and
?h.inflated.
Can you help me with this problem.
Thank,
Trinh
2015-10-05 23:09 GMT+07:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
Hi Trinh
the inflated.nofix files are the ones before the topology fixer
so they will always have defects in them
cheers
Bruce
On Mon, 5 Oct 2015, Thục Trinh wrote:
Hi Bruce,
I did check the output recon by using
mris_euler_number, all the results of
?h.pial, ?.white and also ?h.inflated returned with:
0 holes. But the result
from lh.inflated.nofix was: 28 holes.
When I load the 3D images of ?h.inflated.nofix in
freeview, it appears alot
of holes and also handles errors.
I wonder about the differences between ?h.inflated
and ?h.inflated.nofix. If
we want to estimate the quality of recon output,
what images we should use?
Thanks and Have a nice day,
Trinh
2015-10-02 19:33 GMT+07:00 Bruce Fischl
<fis...@nmr.mgh.harvard.edu>:
Hi Trinh
can you just attach the images? Your link
didn't work for me.
You can check the topology of the surface
computationally using
mris_euler_number. You might also try moving
backwards/forwards
a few slices to try to understand what is
going on.
cheers
Bruce
On Fri, 2 Oct 2015, Thục Trinh wrote:
[icon_10_generic_list.png]
NCP140539_2_recon.rar
Hi Freesurfer Experts,
We are on the process of troubleshooting
our
subjects's recon and we came
across with this error that we can not
determine
what kind of problem this
is:
It seems there is no white matter and
pial errors on
all slices as we check
on three different views
(sagital,coronal and
axial);however, when we load
rh.inflated.nofix surface on both
freeview and
tksurfer, there is a big
difference that at the frontal cortex
(area near the
medial wall), it
appears a handle error and also some
hole errors on
freeview while it does
not on tksurfer.
Would you explain how it is visualized
that makes us
so confused to
troubleshoot since we can not find
anything wrong on
white matter volume to
be fixed?
Here is our data,
Have a nice day,
Trinh
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