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
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