Does it affect the aseg with respect to the GCA registration? Is so, how perfect does the strip need to be to avoid biasing the aeg results, eg., are small portions of the meninges or skull around the top of the cortex going to affect the results much? I now they can affect the pial surface, but I'd prefer to edit that after the surfaces are created. Thanks again! Alex
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sat 9/10/2005 10:56 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Skull stripping Hi Alex,
if the strip removes the cerebellum, then the aseg stuff will fail (if you're using it). If you aren't it doesn't really matter.
cheers, Bruce
On Sat, 10 Sep 2005, Fornito, Alexander wrote:
Hi all, Couple of questions re: failures of skull stripping"
- If you edit the brain volume after autorecon1, do you need to re-run autorecon1 again, or van you just continue on to autorecon2?
- Is it a major problem if the strip removes the cerebellum, since it's excluded by the cuttting planes anyway, or does this interfere with finding the cutting planes later on?
Thanks, Alex
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
no, small errors won't be a problem, but no cerebellum will kill it. On Sat, 10 Sep 2005, Fornito, Alexander wrote:
Does it affect the aseg with respect to the GCA registration? Is so, how perfect does the strip need to be to avoid biasing the aeg results, eg., are small portions of the meninges or skull around the top of the cortex going to affect the results much? I now they can affect the pial surface, but I'd prefer to edit that after the surfaces are created. Thanks again! Alex
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sat 9/10/2005 10:56 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Skull stripping Hi Alex,
if the strip removes the cerebellum, then the aseg stuff will fail (if you're using it). If you aren't it doesn't really matter.
cheers, Bruce
On Sat, 10 Sep 2005, Fornito, Alexander wrote:
Hi all, Couple of questions re: failures of skull stripping"
- If you edit the brain volume after autorecon1, do you need to re-run autorecon1 again, or van you just continue on to autorecon2?
- Is it a major problem if the strip removes the cerebellum, since it's excluded by the cuttting planes anyway, or does this interfere with finding the cutting planes later on?
Thanks, Alex
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Fornito, Alexander