Dear All,
this is very basic. I have Analyze volumes, and I was suggested to use -notal-check to bypass the 3rd recon step. I wanted to make sure skipping the T registration step would not have the potential to mess up the spherical registration in autorecon3 in any way on a case by case basis. I do not want to spend time in tkregister2 unless is necessary for the spherical registration step.
Also, I anticipate losts of pial edits (let's exclude the wm edits/cp), and I wanted to make sure different command scenarios are correct:
1. recon-all -autorecon1 -subjid edit pia, save brainmask.mgz recon-all -autorecon2 -autorecon3 -subjid
2. recon-all -autorecon1 -autorecon2 -subjid edit pia, save brainmask.mgz recon-all -autorecon2-pial -autorecon3 -subjid (preferred)
3. recon-all -subjid edit pia, save brainmask.mgz recon-all -autorecon-pial -subjid
Please comment, thank you, Octavian