Thanks. So the very first step I'll run recon-all -all, then I'll do all my corrections and rerun just recon-all -autorecon2-cp -autorecon3 ... Is that right? Cheers Claudia
2013/6/5 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Claudia
recon-all -autorecon2-cp -autorecon3 ...
will run everything the autorecon2-wm and autorecon2-pial would and more, so you can just run that.
cheers Bruce
On Wed, 5 Jun 2013, Claudia Dacquino wrote:
Hi everyone,I'm sorry, this is a probably very basic question, but I'm a
little bit confused about the recon-all correct flowchart.
I mean, the first step is recon-all -s <subjid> -all (comprising autorecon1, autorecon2 and autorecon3), correct?
After this step if I want to add control points then I have to re-run: recon-all -s <subject> -autorecon2-cp -autorecon3
The same if I want to edit pial surface:
recon -all -s <subject> -autorecon2-pial -autorecon3
Or to edit white matter:
recon-all -s <subject> -autorecon2-wm -autorecon3.
Is that correct?
Is there a system to reduce processing time once I've run eh first step (rec on-all -s -all)?
I mean if I want to add control points, then to edit pial surface and white matter, have I to do the three processes separately, or there is a way to do the three things at once and then running just one autorecon?
If that is permissible, which is the correct command line at the end of the porcess?
I'm sorry for the confusion.
Thanks in advance to everyone.
Claudia
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