why don't you tar and gzip the whole subject dir and upload it to our ftp
site and we will take a look
cheers
Bruce
On Tue, 1 May 2018, Miguel Ángel Rivas
Fernández wrote:
External Email - Use Caution
Hi Bruce,
The problem is that the reconstruction of the pial surface is incorrect. I
tried to put control
points on some voxels but did a wrong reconstruction because in this region
there is no voxel with
an intensity between 95-110. How can I improve the reconstruction of the pial
surface (in this case
extend) without modifying the boundaries of wm? . Sorry, I read the answer you
gave to Saum but I
could not understand very well how to modify the statistics that FreeSurfer
does in the
mri_make_surfaces.
Hi Saum
it is, but you need to figure out why it isn't getting out far enough. The
easiest way is to
override the intensity statistics that are computed automatically in
mris_make_surfaces. You can see
them if you look in your recon-all.log. For example if the lowest value gm is
allowed to be at the
pial surface is too high, then it will settle too far in
Thanks,
Cheers,
2018-04-29 17:33 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
that looks like a big temporal lobe bias field to me. Is the WM in the
temporal lobes
significantly darker than 110? I can't tell if some of the stuff in e.g.
the left medial
temporal lobe is WM or GM. Try putting some control points in regions
where the
intensity is in say [95, 110) and see if that helps
cheers
Bruce
On Sat, 28 Apr 2018, Miguel Ángel Rivas Fernández wrote:
External Email - Use Caution
Hi guys,
I have the same problem as Saum, I executed the recon-all in several
subjects and I did not obtain a
completely correct segmentation of the pial surface. To solve this
error
could I use the control
points? When I use the control points, will I also be able to
correct the
white matter segmentation?
I send you a image if you want
to check it.
Thank you very much!
Cheers,
[IMAGE]
2018-04-27 21:28 GMT+02:00 Bruce Fischl
<fis...@nmr.mgh.harvard.edu>:
Hi Saum
it is, but you need to figure out why it isn't getting out
far enough.
The easiest way
is to override the intensity statistics that are computed
automatically in
mris_make_surfaces. You can see them if you look in your
recon-all.log. For example if
the lowest value gm is allowed to be at the pial surface is
too high,
then it will
settle too far in
cheers
Bruce
On Fri, 27 Apr 2018, Saum Naderi wrote:
External Email - Use Caution
Hi guys,
I'm having some trouble extending the pial surface of
my bm
volume. I am
aware that the general
procedure for extending the pial is to extend the wm
first and
the pial will
follow. However, is it
possible to extend the pial surface without affecting
the wm
boundary?
Thanks,
Saum
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