Hi Rujing,
Even if there is some skull/dura left after the skullstrip step in
recon-all, it still may not negatively impact the surfaces. It might be
worth running the remaining recon-all steps to see how the surfaces turn
out.
If you want to swap-in a better skullstripped volume into the recon-all
stream then you just need to replace the brainmask.mgz and continue with
autorecon2 and autorecon3.
Keep in mind that the new brainmask.mgz volume still needs to be in the
conformed anatomical space, so use the T1.mgz or brainmask.mgz to create
the improved skullstrip volume which will replace the existing
brainmask.mgz.
-Louis
On Mon, 2 Dec 2013, Rujing Zha wrote:
Dear all,
Part of subjects 3d images cannot be stripped skull and neck properly in
recon-all default. I have got the brain volume mask, how I can using the
existing proper mask to help strip skull in recon-all and next workflow?
Thanks.Any reply will be appreciated.
All the best.
2013-12-02
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Rujing Zha
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