I&#39;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?  <br>
<br>I&#39;m currently stuck on autorecon2&#39;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&#39;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?    <br>