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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