Hi Antonin,

max does not constrain thickness. The location of the max is constrained to be within 2*max for every iteration, so it will constrain how far outwards it searches. But it will be done at each scale, so it can still deform a long way.

We initialize the surface processing in long with the surface from the base. But we don’t use the pial from base directly, instead we shrink it a little first and start from there.

Not sure about the last question (difference between orig and prig-white parameters).

Best, Martin

On Nov 14, 2016, at 10:17 PM, Antonin Skoch ansk@ikem.cz wrote:

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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer