From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fischl, Bruce
Sent: Wednesday, June 23, 2021 4:53 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] how to shrink WM surface in one region
Hi Lara
Can you send us some pictures? The answer depends on why the white
@nmr.mgh.harvard.edu
Subject: [Freesurfer] how to shrink WM surface in one region
External Email - Use Caution
Hi everyone,
Very quick question - I need to shrink the white matter surface in a very
specific (constrained) region. Can you please confirm that the right way to go
about
External Email - Use Caution
Hi everyone,
Very quick question - I need to shrink the white matter surface in a very
specific (constrained) region. Can you please confirm that the right way to go
about this is to (1) manually remove voxels from the WM volume in freeview,
then
Hi Mike
sorry, I never really documented it. Essentially they provide limits on
the allowable intensities of the various tissue classes at the different
boundaries (gray/white and pial). Unless those constraints are satisfied it
will not try to place the boundary in that region
cheers
Bruce
Hi Bruce,
I was wondering if there is info somewhere about what each of those 7 MIN_
and MAX_ variables control regarding the positioning of the white and pial
surfaces?
thanks,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the
Have a look at mris_make_surfaces.c, this is how I learned about most of
this stuff as the code is pretty well commented (and Bruce telling me
things).
Peace,
Matt.
On 9/12/14, 11:01 PM, Harms, Michael mha...@wustl.edu wrote:
Hi Bruce,
I was wondering if there is info somewhere about what
Dear Freesurfers,
After running recon-all, the wm surfaces are too close to the pial surface,
some gray matter is segmented as white matter as seen in the attached
picture (red cross: a bigger cortical part is included in the white matter).
How can I shrink the wm surface?
Thank you for your
-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Andrea Horváth
Sent: Tuesday, September 09, 2014 7:08 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] how to shrink wm surface
Dear Freesurfers,
After running recon-all, the wm surfaces are too close
Hi Andrea
what is the background image? This is usually either a failure of the
intensity normalization or of the surface deformation/segmentation to
adaptively estimate the underlying intensity distributions of the
gray/white matter. If you look in recon-all.log for that subject you will
