Dear experts, I am trying to understand how the pial and white surfaces are generated in longitudinal stream using information from the reconstructed base template (freeSurfer development version).
In longitudinal stream, apart from the -orig, -orig_pial and -orig_white there are also parameters -long and -max 3.5. May I ask what is the significance of these parameters? -max 3.5 means constraining cortical thickness to 3.5 mm? Why this constraint is applied specifically in longitudinal stream? In mris_make_surfaces.c I found that -long means that initial pial vertex positions are set between final white and orig pial, slightly inside orig_pial. What is the significance of this setting in longitudinal stream? Last question, not related specifically to longitudinal stream: What is the difference between -orig and -orig_white parameters of mris_make_surfaces? From the reading of source codes (quite tough to me) I got an impression that from -orig the gray and white matter histogram values are computed whereas -orig_white defines initial position of the vertices in the first iteration (which, for some reasons, does not necessary has to be identical to -orig). Am I correct? Regards, Antonin Skoch
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