Try setting -max XXX
where XXX is the maximum allowable thickness. It is default to 5, so try
something large
On 2/21/2020 11:36 AM, CiRong Liu wrote:
External Email - Use Caution
Dear experts of the freesurfer,
I was trying to create the white matter and pial surfaces of
the cerebellum of the marmoset, based on ultra-high (80um) resolution
ex-vivo images.
I manually segment the cerebellum into the white matter and the gray
matter and change the header information to 1mm.
Based on the manual segmented files, I created white matter surfaces
(rh.orig).
I tried to use the mris_make_surfaces to expand the white matter to
create the matched pial surface.
However, the /mris_make_surfaces/ failed to push the surface enough.
See the attached files and screenshots.
I tried smoothing the segmentation, enhancing the contrasts, and
tested different expert option (for example: -max_csf 0.1
-min_gray_at_csf_border 1)
This was this best I got, but still cannot get an optimal result (not
pushed enough):
/mris_mask_surfaces -max_csf 0.1 -min_gray_at_csf_border 1 -orig_wm
orig -orig_pial orig -noaseg -noaparc -T1 ceb_sm marmosetceb rh /
Since I have already manually segmented the cerebellum, *is there a
way to force the /mris_make_surfaces/ to expand to the boundary of the
image?*
The files can be download to replicate what I did:
https://pitt.box.com/s/6269a9mnwbs6zi0azn08dn55u47yfa7i
Thank you very much!
Best Regards, CiRong Liu
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