Hello,
I've got a data set that has already been skull stripped; how should I run this through the recon_all process? Is there a flag to skip the skullstripping stage?
Thanks, Paul
Paul,
You can add the -noskullstrip flag to recon-all -autorecon1.
Just be sure, when -autorecon1 is complete, to make a symbolic or copy of T1.mgz to brainmask.auto.mgz, and a link from brainmask.auto.mgz to brainmask.mgz. Also make sure that that brainmask.mgz looks like what is expected of brainmask.mgz (by comparing against the sample subject bert). The cerebellum should be intact, and very little, in any, skull should remain.
Nick
On Thu, 2007-09-27 at 10:29 -0700, Paul Greenberg wrote:
Hello,
I've got a data set that has already been skull stripped; how should I run this through the recon_all process? Is there a flag to skip the skullstripping stage?
Thanks, Paul
you'll also need to make sure it's "conformed" (256^3, 1mm iso, 8 bits/voxel)
On Thu, 27 Sep 2007, Nick Schmansky wrote:
Paul,
You can add the -noskullstrip flag to recon-all -autorecon1.
Just be sure, when -autorecon1 is complete, to make a symbolic or copy of T1.mgz to brainmask.auto.mgz, and a link from brainmask.auto.mgz to brainmask.mgz. Also make sure that that brainmask.mgz looks like what is expected of brainmask.mgz (by comparing against the sample subject bert). The cerebellum should be intact, and very little, in any, skull should remain.
Nick
On Thu, 2007-09-27 at 10:29 -0700, Paul Greenberg wrote:
Hello,
I've got a data set that has already been skull stripped; how should I run this through the recon_all process? Is there a flag to skip the skullstripping stage?
Thanks, Paul
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