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Hi all,
I'm trying -multistrip to improve skull stripping for subjects where incomplete skull strip lead to inaccurate pial surfaces. The command I'm running is: recon-all -multistrip -clean-bm -s <subjID> -no-isrunning
However, multistrip fails. It exits with errors and no new brainmask.mgz files are created. This is independent of the subject. It fails for all. I attached the recon-all.log for one exemplary subject.
In contrast, using -gcut (recon-all -skullstrip -clean-bm -gcut -s <subjID>) works but does not remove the problematic skull fragments in most cases.
Independent of whether -multistrip or -gcut are better suited to improve the skull stripping, I would like to understand why -multistrip fails in my case and what can be done to make it work.
Best, JJ