Hi Mark yes, that should work
cheers Bruce On Thu, 15 Jan 2015, Mark Fletcher wrote:
Dear FreeSurfer Community, I am correcting a lot of brains and am wondering if I can combine two steps? Currently, I first correct pial surfaces by manually deleting voxels (dura, bad skull strip, etc). I then run this command. recon-all -autorecon-pial –subjid randomsubject After finishing this, I add control points (often to the temporal lobe) and then run this command recon-all -autorecon2-cp -autorecon3 -subjid randomsubject Although this works, it would save me a lot of time if I could correct the pial surface and control points at the same time? Meaning, I would open the brain once, delete dura that has been traced wrong, add control points (by making a control.dat file in the tmp folder) and then run one code overnight? I am okay if the computer processing takes a bit longer.... but what is the command (with the correct flags) that I should run? Would it be something like this recon-all -autocron-pial -autorecon2-cp -autorecon3 -subjid randomsubject?? Thanks for your help in advance. -Mark Fletcher UIUC
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