In recon-all, it says you are supposed to use -autorecon2-cp if you use control points. So I wonder why earlier normalization steps also use control points, such as Norm1 and CANormalize. What effect do the control points have in those steps?
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Hi Don,
Nick actually just recently included something to allow you to pass the control points to mri_ca_normalize, so it can help the subcortical segmentation. Nick: what is the new flag?
cheers, Bruce
On Wed, 11 Jul 2007, Don Hagler wrote:
In recon-all, it says you are supposed to use -autorecon2-cp if you use control points. So I wonder why earlier normalization steps also use control points, such as Norm1 and CANormalize. What effect do the control points have in those steps?
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Don,
If the file $subjdir/tmp/control.dat exists, then it is automatically added to the mri_normalize and mri_ca_normalize steps. An explicit flag is not needed.
Nick
On Wed, 2007-07-11 at 21:27 -0400, Bruce Fischl wrote:
Hi Don,
Nick actually just recently included something to allow you to pass the control points to mri_ca_normalize, so it can help the subcortical segmentation. Nick: what is the new flag?
cheers, Bruce
On Wed, 11 Jul 2007, Don Hagler wrote:
In recon-all, it says you are supposed to use -autorecon2-cp if you use control points. So I wonder why earlier normalization steps also use control points, such as Norm1 and CANormalize. What effect do the control points have in those steps?
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So then for redoing a recon with control points, it would be beneficial to start again at the mri_normalize step?
From: Nick Schmansky nicks@nmr.mgh.harvard.edu To: Bruce Fischl fischl@nmr.mgh.harvard.edu CC: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu, Don Hagler dhaglerjr@hotmail.com Subject: Re: [Freesurfer] control points Date: Thu, 12 Jul 2007 15:51:17 -0400
Don,
If the file $subjdir/tmp/control.dat exists, then it is automatically added to the mri_normalize and mri_ca_normalize steps. An explicit flag is not needed.
Nick
On Wed, 2007-07-11 at 21:27 -0400, Bruce Fischl wrote:
Hi Don,
Nick actually just recently included something to allow you to pass the control points to mri_ca_normalize, so it can help the subcortical segmentation. Nick: what is the new flag?
cheers, Bruce
On Wed, 11 Jul 2007, Don Hagler wrote:
In recon-all, it says you are supposed to use -autorecon2-cp if you
use
control points. So I wonder why earlier normalization steps also use
control
points, such as Norm1 and CANormalize. What effect do the control
points
have in those steps?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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the first mri_normalize is really only for the talairaching and the skullstrip, so if those worked fine you don't need to. You could start at the ca_normalize again I suppose, but of course it will take a while :).
On Thu, 12 Jul 2007, Don Hagler wrote:
So then for redoing a recon with control points, it would be beneficial to start again at the mri_normalize step?
From: Nick Schmansky nicks@nmr.mgh.harvard.edu To: Bruce Fischl fischl@nmr.mgh.harvard.edu CC: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu, Don Hagler dhaglerjr@hotmail.com Subject: Re: [Freesurfer] control points Date: Thu, 12 Jul 2007 15:51:17 -0400
Don,
If the file $subjdir/tmp/control.dat exists, then it is automatically added to the mri_normalize and mri_ca_normalize steps. An explicit flag is not needed.
Nick
On Wed, 2007-07-11 at 21:27 -0400, Bruce Fischl wrote:
Hi Don,
Nick actually just recently included something to allow you to pass the control points to mri_ca_normalize, so it can help the subcortical segmentation. Nick: what is the new flag?
cheers, Bruce
On Wed, 11 Jul 2007, Don Hagler wrote:
In recon-all, it says you are supposed to use -autorecon2-cp if you use control points. So I wonder why earlier normalization steps also use
control
points, such as Norm1 and CANormalize. What effect do the control
points
have in those steps?
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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