Try using mri_label2vol with the ribbon.mgz file. That has a 
segmenentation of everything inside the white surface.

On 08/10/2017 03:58 PM, Rockers, Elijah D. wrote:
> I am attempting to create a volume from a surface. My ultimate goal is 
> to obtain a mask that includes everything "inside" the white matter 
> surfaces. wm.mgz is close, but it would nicer to just get a mask from 
> lh.white and rh.white. I would like these masks to be in the subject's 
> native space. However I try the following command and see the 
> resulting error:
> mri_surf2vol --o coleMRI06162006/mri/lh.white.mask.mgz --mkmask --hemi 
> lh --identity coleMRI06162006 --template coleMRI06162006/mri/orig/orig.mgz
> gdiagno = -1
> Using identity matrix for registration
> mghRead(coleMRI06162006/mri/orig/orig.mgz, -1): could not open file
> mri_surf2vol ERROR: reading coleMRI06162006/mri/orig/orig.mgz header
> I'm obviously doing something wrong here, but I'm not sure what needs 
> to change. I used --identity because native space, and it wouldn't let 
> me run the command without specifying --template, which I'm not sure I 
> understand, because, again, target is native space. Please illuminate me,
> Thank you,
> - Eli
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Douglas N. Greve, Ph.D.
MGH-NMR Center
Phone Number: 617-724-2358
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