Hi Antonin, we start slightly inside as surfaces expand more easily than shrink. This way even for the further atrophied time points there is a higher chance that it will be slightly inside it’s final position.
The mris_longitudinal_surfaces is over 11 years old and was used for testing other approaches back then. Best, Martin > On Nov 22, 2016, at 11:24 PM, Antonin Skoch <a...@ikem.cz> wrote: > > Dear Martin, > > thank you for the explanations, and sorry, I missed your previous response. > > Just I am wondering, what is the reason of the shrinkage? Why not to start > directly from pial surface of the base? > > And, I also found a binary mris_longitudinal_surfaces, which is, however, not > used in recon-all. What is the significance of this binary? > > Antonin > > ------------------------------- > > 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 at ikem.cz > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> 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 at nmr.mgh.harvard.edu > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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.
