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 _______________________________________________ Freesurfer mailing list Freesurfer at nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Antonin
in the case of severe atrophy or a long period between scans the pial surface from time 1 may be far enough outside the pial surface of time 2 that the deformation cannot recover it. We have found that starting it a bit inside makes it more robust.
As for the mris_longitudinal_surfaces there are lots of binaries that we develop and try out that aren't used in recon-all but might be some day
cheers Bruce
On Tue, 22 Nov 2016, Antonin Skoch 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*m ax 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 ther e.
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 ve rsion).
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 appli
ed 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 significan ce 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 sourc e 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 vertic es in the first iteration (which, for some reasons, does not necessary has to be identica l 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
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 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@nmr.mgh.harvard.edu
-
Antonin Skoch -
Bruce Fischl -
Martin Reuter