the -affine flag was only for some debugging and is currently not supported. It may also not do what you think it does. It will remove scaling difference between your time points. This makes sense if you have test-retest scans and want to remove scanner calibration scaling problems. It will not be the right tool, if heads grow (as a longitudinal analysis will only provide measurements after global scaling is removed between time points).

On 7. Oct 2020, at 10:54, Marisa Johanna Nordt <mnordt@stanford.edu> wrote:

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Hi,

I have a question about the lta files from the longitudinal pipeline (using the –affine flag). Instead of just one .lta file from each timepoint to the template 3 different .lta files are saved
-tp1_to_templ_norm.lta,
-tp1_to_templ_affine.lta,
-tp1_to_templ.lta

Is the one created last (tp1_to_templ.lta) the final lta-file that I can use to align additional files from tp 1 to the template?

Thanks a lot!
Marisa

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