hi claudia,

do your all of your (cp, pial, wm) editing and once complete then you can 
combine all three steps you have below into one step:

recon-all –s <subject> -autorecon2 –autorecon3

-robert


From: Claudia Dacquino 
<claudia.dacqu...@gmail.com<mailto:claudia.dacqu...@gmail.com>>
Date: Wednesday, June 5, 2013 5:45 AM
To: freesurfer mailing list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] processing flow

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 
(recon-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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