Hi Ajay
Florent Segonne developed some volumetric topology correction algorithms
as well as surface-based ones when he was here. Try
mri_topologycorrection and see how it works for you (although be warned
that we haven't tried it in ages)
cheers
Bruce
On Mon, 21 Mar 2016,
Ajay Kurani wrote:
Hi Freesurfer experts, I wanted to create a Freesurfer surface on some of
the aseg ROIs. I was able to run mri_tesselate, mris_smooth, mris_inflate
and mris_sphere some of the subcortical volumes for creating a surface.
The mri_sphere had a big chunk that was deleted and so I wanted to run
mris_fix_topology to fix this issue. In trying to run this command it
appears that mris_fix_topology tries to correct based off of a brain sphere
(which this ROI is clearly not) and therefore it fails. I plan to then run
subsequent steps such as mris_euler number and mris_remove_intersections
1) Is there any way to fix the topology of this ROI using freesurfer tools
or a way to work around this issue? Do you feel the sphere is needed for a
small subcortical surface (ie globus pallidus) or is this really more for
complex structures such as cortical surfaces?
2) Is there a recommended set of steps to accomplish creating a surface from
the ROI that is different from what I stated?
Thanks,
Ajay
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