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 <a...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
