I'm trying to run recon-all on brains that have already been skullstripped and had their necks removed. I ran autorecon1 without the skullstrip steps. To generate brainmask.mgz I just created a renamed copy of T1.mgz. Is this okay?
I'm currently stuck on autorecon2's segstats step. (For autorecon2 I opted out of the neck removal.) At the segstats step I get an error that says that I am missing transforms/talairach_with_skull.lta. talairach_with_skull.lta is created from autorecon1's skullstripping step, but I skipped that step because my brain is already skullstripped. How would I generate this file so that I may proceed with segstats?
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