Hi,
I wonder if there is a way for mri_robust_template to perform iterative registration with 9 DOF rather than 6-7 default. The rational is to allow for a bit of scaling to adjust for potential scanner drifts in a longitudinal study over years.
Thanks, Arman
Hi Arman,
should be possible by passing the - - affine flag. I think I also experimented around with a -base-affine flag to recon-all for that (instead of -base). It is experimental!
Best, Martin
On 07 Apr 2017, at 13:34, Arman Eshaghi arman.eshaghi@gmail.com wrote:
Hi,
I wonder if there is a way for mri_robust_template to perform iterative registration with 9 DOF rather than 6-7 default. The rational is to allow for a bit of scaling to adjust for potential scanner drifts in a longitudinal study over years.
Thanks, Arman _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Martin. Should I be worried about affine transform masking out the global atrophy if I am using the whole brain (no skull stripping)?
Arman
On Wed, Apr 12, 2017 at 9:36 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:
Hi Arman,
should be possible by passing the - - affine flag. I think I also experimented around with a -base-affine flag to recon-all for that (instead of -base). It is experimental!
Best, Martin
On 07 Apr 2017, at 13:34, Arman Eshaghi arman.eshaghi@gmail.com wrote:
Hi,
I wonder if there is a way for mri_robust_template to perform iterative
registration with 9 DOF rather than 6-7 default. The rational is to allow for a bit of scaling to adjust for potential scanner drifts in a longitudinal study over years.
Thanks, Arman _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Yes, that is why it is experimental.
However, global atrophy will affect the ventricles (they are growing) which is an effect in the opposite direction, so maybe it cancels out to some extend.
Best, Martin
On 12 Apr 2017, at 23:55, Arman Eshaghi arman.eshaghi@gmail.com wrote:
Thanks Martin. Should I be worried about affine transform masking out the global atrophy if I am using the whole brain (no skull stripping)?
Arman
On Wed, Apr 12, 2017 at 9:36 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> wrote: Hi Arman,
should be possible by passing the - - affine flag. I think I also experimented around with a -base-affine flag to recon-all for that (instead of -base). It is experimental!
Best, Martin
On 07 Apr 2017, at 13:34, Arman Eshaghi <arman.eshaghi@gmail.com mailto:arman.eshaghi@gmail.com> wrote:
Hi,
I wonder if there is a way for mri_robust_template to perform iterative registration with 9 DOF rather than 6-7 default. The rational is to allow for a bit of scaling to adjust for potential scanner drifts in a longitudinal study over years.
Thanks, Arman _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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