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

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*From:* Martin Reuter [mreuter@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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