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

 

 

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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