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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:
https://secure-web.cisco.com/1Blsa_5fBePXLqTD4MyXB0MVZ8BfrqXwEgfuiFRtv-42VQP...
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