I¹ve been going over the tutorials, but my question remains is T1 skull stripped? It seems to check skull stripping brain.mgz is loaded as the main volume with T1.mgz as the aux. Flipping back and forth (control 1/control 2) is used to check the stripped brain.mgz. This implies T1 has the skull still (yet my T1 images are all skull stripped). Thanks.
Cliff
------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
Hi Cliff,
there's an interim dev version in which T1 is created with a skull then regenerated without one. This was a mistake on our part, and will go away in the new release (coming soon!), in which T1 will have the skull on it. Sorry for the confusion.
cheers, Bruce
On Thu, 12 Jan 2006, Clifford A. Smith, PhD wrote:
I¹ve been going over the tutorials, but my question remains is T1 skull stripped? It seems to check skull stripping brain.mgz is loaded as the main volume with T1.mgz as the aux. Flipping back and forth (control 1/control 2) is used to check the stripped brain.mgz. This implies T1 has the skull still (yet my T1 images are all skull stripped). Thanks.
Cliff
Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
Thanks. I've been having a panic attack trying to resolve this (or maybe it's just too much coffee!).
------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Thu, 12 Jan 2006 17:12:31 -0500 (EST) To: "Clifford A. Smith, PhD" csmith13@rush.edu Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Simple ? about T1.mgz
Hi Cliff,
there's an interim dev version in which T1 is created with a skull then regenerated without one. This was a mistake on our part, and will go away in the new release (coming soon!), in which T1 will have the skull on it. Sorry for the confusion.
cheers, Bruce
On Thu, 12 Jan 2006, Clifford A. Smith, PhD wrote:
I¹ve been going over the tutorials, but my question remains is T1 skull stripped? It seems to check skull stripping brain.mgz is loaded as the main volume with T1.mgz as the aux. Flipping back and forth (control 1/control 2) is used to check the stripped brain.mgz. This implies T1 has the skull still (yet my T1 images are all skull stripped). Thanks.
Cliff
Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
oh, our fault. Sorry :<.
Bruce On Thu, 12 Jan 2006, Clifford A. Smith, PhD wrote:
Thanks. I've been having a panic attack trying to resolve this (or maybe it's just too much coffee!).
Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Thu, 12 Jan 2006 17:12:31 -0500 (EST) To: "Clifford A. Smith, PhD" csmith13@rush.edu Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Simple ? about T1.mgz
Hi Cliff,
there's an interim dev version in which T1 is created with a skull then regenerated without one. This was a mistake on our part, and will go away in the new release (coming soon!), in which T1 will have the skull on it. Sorry for the confusion.
cheers, Bruce
On Thu, 12 Jan 2006, Clifford A. Smith, PhD wrote:
I¹ve been going over the tutorials, but my question remains is T1 skull stripped? It seems to check skull stripping brain.mgz is loaded as the main volume with T1.mgz as the aux. Flipping back and forth (control 1/control 2) is used to check the stripped brain.mgz. This implies T1 has the skull still (yet my T1 images are all skull stripped). Thanks.
Cliff
Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, I've got a few reltively simple questions that I'm sure I've seen the answers to before but can't seem to find them again. What is the difference between ?h.orig, ?h.white, and ?h.smoothwm? Which one is automatically brought up in tkmedit when ?h.pial is loaded as a surface? Which is usd in the thickness calculations? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
?h.white is the surface that is used for morphometry (e.g. thickness) and is brought up in tkmedit. You can safely ignore the others.
Bruce On Fri, 13 Jan 2006, Fornito, Alexander wrote:
Hi, I've got a few reltively simple questions that I'm sure I've seen the answers to before but can't seem to find them again. What is the difference between ?h.orig, ?h.white, and ?h.smoothwm? Which one is automatically brought up in tkmedit when ?h.pial is loaded as a surface? Which is usd in the thickness calculations? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
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 -
Clifford A. Smith, PhD -
Fornito, Alexander