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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