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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