Hi Chris,
for the motion correction step there is no bias-field correction. First
it is assumed that bias field is not very different (scans are from the
same session) and also the robust register can down-weigh regions that
differ a lot.
However the methods estimates a global intensity scale parameter
simultaneously during the registration to adjust intensity values across
the images (that's in the robust register paper).
Best, Martin
On 06/27/2013 06:45 AM, Parker, Christopher wrote:
Hi Martin,
Are the images bias-field corrected before registration in recon-all?
If so, which method is used for this? Is there a paper for
reference/citation also?
Many Thanks,
Chris
------------------------------------------------------------------------
*From:* Martin Reuter [mreu...@nmr.mgh.harvard.edu]
*Sent:* 25 June 2013 18:53
*To:* Bruce Fischl
*Cc:* Parker, Christopher; freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] freesurfer registration
Hi Chris,
we actually do use my robust registration tool for it since a while
(FS 5.0, Aug 2010), replacing FLIRT which was used before. Here is the
citation:
M. Reuter, H.D. Rosas, B. Fischl. *Highly Accurate Inverse Consistent
Registration: A Robust Approach*. /NeuroImage 53(4):1181-1196, 2010/.
It is a robust rigid registration, using the tukey biweight function
on the residuals. The statistical robustness makes it less sensitive
to outliers (e.g. differences in jaw, neck, eye regions) by
identifying regions with local differences during the registration and
reducing their influence on the registration. This leads to very
accurate alignment in the regions that do not change (the brain).
Cheers, Martin
On 06/25/2013 12:05 PM, Bruce Fischl wrote:
yes, it's rigid and used to be sum of squares but in the newer versions we
will be using Martin's robust registration (which is a tukey biweight
instead of SSE)
On Tue, 25 Jun 2013, Parker, Christopher wrote:
Hi,
I understand that the recon-all script registers and then averages two
anatomical images (after bias field correction) if two are provided in the
"orig" folder, before performing the other parcellation stages. I am writing
a report and it might be good to mentioned what registration is used. I'm
guessing this is a rigid registration using sum of squared differences cost
function?
Best,
Chris
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--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web :http://reuter.mit.edu
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--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web : http://reuter.mit.edu
_______________________________________________
Freesurfer mailing list
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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 . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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