Hello all
I have the freesurfer automatic hippocampus
segmentation for some subjects. It seems that the
segmentation is not bad. I have produced the binary
masks (after labels generation in tksurfer)with the
following command:
mri_label2vol
--label label/lefthipoca.label
--temp mri/orig.mgz
--o lefthipoca.img
I have loaded the lefthipoca.img mask in matlab and
used the standard matlab isosurface algorithm to
triangulate the contours of the binary mask.
The problem is that the resulting surface although no
topological defects and no boundaries does not have
spherical topology (euler number<2).
Is it a consequence of imperfections in the freesurfer
segmentation? How can I correct it?
I have seen that with litter volumetric smoothing of
the mask I get surfaces with spherical topology after
the triangulation, but the structure volume is
remarkable increased after the smoothing.
Any tip is welcome
In advance Thank you
Jorge
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