Hi Miao

try using mris_fill instead. I think it defaults to 0.5mm resolution, but this can be changed with -r <res>

cheers Bruce On Thu, 5 Sep 2019, Jingya Miao wrote:

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Hello Freesurfer Developers, I am trying to generate a solid volume out of the lh/rh.pial-outer-smoothed file.

I was able to get just the surface in .nii format by using:

  mri_surf2vol --hemi lh --surf pial-outer-smoothed --mkmask --reg
  mri/register.dat --o surfsmoothed.nii --template mri/T1.nii
  --subject BerA

I also attempted to use --fillribbon

  mri_surf2vol --surfval
  $SUBJECTS_DIR/Berger_Andrew/surf/lh.pial-outer-smoothed
  --fillribbon --reg mri/register.dat --o smoothedfill.nii
  --template T1.nii --subject BerA 

gdiagno = -1

ERROR: cannot recognize the type of /Users/mah.ali/freesurfer/subjects/Ber

A/surf/lh.pial-outer-smoothed

I am wondering what would be a good way to generate a solid volume out of the pill-outer-smoothed files.

Thank you,

Miao