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Hi Jan
If you create a family template you will only be able to compare within family, unless you also align the templates I guess?
-nonorm will disable z-normalization of curv and sulc. We typically start with a single subject atlas, do a nonlinear (but highly regularized) warp to it, then rebuild the atlas and re-register. We do have a prototype of a more principled procedure but it won't be ready for a few months
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Koten, Jan Willem (jan.koten@uni-graz.at) Sent: Monday, May 8, 2023 8:01 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mris_register options
External Email - Use Caution Dear Doug Dear Bruce
Martin Reuter suggested me to write you since you are familiar with true inner workings of free surfer. In my project I try to create a family specific template that is based on three or more family members. We try to avoid the bias that may arise by choosing one family member as a target. There is procedure that tries to this described in:
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We found out that family specific templates result in better alignment among family members when compared to the standard fs average template. The creation of a template depends on the mris_register command that has several options that can be manipulated. However, we do not know what those options are doing in detail
What is the initial sulcal alignment? Is this a rigid alignment procedure? Maybe a hard spherical rotation based on least squares algorithms?
What is the final curve alignment? Is this a non-linear alignment procedure?
If sulcal alignment is rigid, why does it take three times as long as non-linear curv alignment?
What is normalization in context of mris_register which can be disabled trough the -nonorm step?
Does the spring factor affect how much the Individual scul/curv maps are aligned with the family template? And if the latter is the case what is a reasonable spring value if you want to obtain individuals that are as closely matched to the family template as possible?
Thank you in Advance Many greetings from Austria
Jan