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 <ansk@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> 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
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