On Wed, 2013-03-13 at 10:52 -0700, Mehul Sampat wrote:
> ps: just wanted to add a clarification to my question. The two
> scenarios are:
> Scenario A:
> 1. recon-all -s <subject> -autorecon1 -autorecon2 -autorecon3
> 2. add control points
> 3. recon -all -s <subject> -autorecon2-cp -autorecon3
>
>
> Scenario B:
> 1. recon-all -s <subject> -autorecon1 -autorecon2
> 2. add control points
> 3. recon -all -s <subject> -autorecon2-cp -autorecon3
>
>
> If Scenario B is permissible, the advantage is that, -autorecon3 is
> only run once thus saving
> a few hours of computation.
>
>
> Thanks
> Mehul
>
> On Wed, Mar 13, 2013 at 10:35 AM, Mehul Sampat <
mpsampat@gmail.com>
> wrote:
> Hi Folks,
> Based on the tutorials, we normally run full recon-all
> pipeline; then add control points if required and then
> run -autorecon2-cp and -autorecon3 again.
>
>
> Recently, I was looking at the process flow table:
>
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
> and I have two questions:
>
>
> 1. From this table it seems like ?h.white is created in
> autorecon2 and ?h.pial is created in autorecon3.
> However, when i run recon-all -s subj -autorecon1 -autorecon2
> i see that ?h.pial is also already created.
> Does this mean I am interpreting the process flow table
> incorrectly or is there an error in the table ?
>
>
> 2. Also if ?h.pial and ?h.white are already created at the end
> of autorecon2; then can we add control
> points at immediately after autorecon2 ? This way we would
> need to run autorecon3 only once and save resources.
>
>
> Or am I missing something and is it that one must run
> -autorecon2 and -autorecon3 and then add control points
> and then run -autorecon2-cp and -autorecon3 again.
>
>
> Thanks
> Mehul
>
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