Yes, it does. Prior to v6, the brain mask was created by the FSL BET
program, which did not depend on the registration. V6 now maps the
brainmask from the FS analysis into the subject space, which does depend
on the registration
On 07/11/2017 02:36 PM, Li Guo wrote:
> Dear freesurfer developers,
>
> I’d like to ask about an error I encountered in Freesurfer v6.0 with
> mkbrainmask-sess. I am using macOS Sierra.
> Here is the error:
>
> error:"ERROR: cannot find
> /Users/lguo15/Documents/MATLAB/fMRI_P3/Fisch_P3_01/bold/register.dof6.lta,
> you might need to run register-sess”
>
> The error goes away if I run register-sess before mkbrainmask-sess.
> However, my lab mates use v5.3 and ran the exact same preprocess
> pipeline without this error. The order for them is mkbrainmask-sess
> first and register-sess later.
>
> I’d like to ask whether it is true that maybe in v6.0 mkbrainmask-sess
> now depends on register-sess to generate the register.dof6.lta file?
> Or how should I interpret this? Does running registration and masks
> have some fixed order at all or it doesn’t matter?
>
> Best,
> Li
>
>
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