I tried that, but then it also runs steps from autorecon1 (tailararch
check, nu, etc)
On Fri, Mar 2, 2012 at 2:40 PM, Allison Stevens Player <
astev...@nmr.mgh.harvard.edu> wrote:
> Okay, I'll look into it and fix the wiki page if needed. However, -make
> all should do the same for you.
> Allison
Okay, I'll look into it and fix the wiki page if needed. However, -make all
should do the same for you.
Allison
On Mar 2, 2012, at 8:23 AM, Martijn Steenwijk
wrote:
> Hi Allison,
>
> But when I run -autorecon-cp it complains that the option does not exist. I'm
> using FS5.1..
>
> msteenwj@
Ok, thanks!
On Fri, Mar 2, 2012 at 2:37 PM, Bruce Fischl wrote:
> yes, it will recognize and use the control points. autorecon2-cp is a
> subset of autorecon2 so no need to rerun it.
>
>
> cheers
> Bruce
>
>
> On Fri, 2 Mar 2012, Martijn Steenwijk wrote:
>
> Okay :-). Last question then, how abo
yes, it will recognize and use the control points. autorecon2-cp is a
subset of autorecon2 so no need to rerun it.
cheers
Bruce
On Fri, 2 Mar 2012, Martijn Steenwijk wrote:
Okay :-). Last question then, how about skull strip correction.
If I understood well, it is advisable to first add con
Okay :-). Last question then, how about skull strip correction.
If I understood well, it is advisable to first add control points and then
correct the skull strip. Will the option set -autorecon2 -autorecon3 (as
indicated in the wiki to be runned after manual skull strip correction)
also recognize
Hi Martin
yes, you are right, that is a typo. And rerunning autorecon2 is
sufficient since it is a superset of autorecon2-cp (and will detect the
existence of control points, and use them)
cheers
Bruce
On Fri, 2 Mar 2012, Martijn
Steenwijk wrote:
Dear all,
On http://surfer.nmr.mgh.harvard
Hi Allison,
But when I run -autorecon-cp it complains that the option does not exist.
I'm using FS5.1..
msteenwj@lnx-rad-03 freesurfer51 % recon-all -subjid P102_corr -autorecon-cp
ERROR: Flag -autorecon-cp unrecognized.
-subjid P102_corr -autorecon-cp
Linux lnx-rad-03 2.6.18-92.1.18.el5 #1 SMP W
Hi Martijn,
autorecon-cp is correct, we start the process a bit earlier now. But even
better, regardless of what edits you make, you can rerun with "recon-all -make
all" and it will start at the earliest needed step. (Although running from
autorecon2 after the skullstrip fix is correct as well).
Dear all,
On http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction it is
indicated that -autorecon-cp should be added if control points are added.
Shouldn't this be -autorecon2-cp?
Furthermore, suppose control points are added and -autorecon2-cp has been
runned. If I then correct the
