Hi Kalyan
usually improving the wm surfaces results in improved pial surfaces. If
not, it typically means something went wrong. If you upload a subject and
email me and Ani the coordinates of a spot (or spots) you are having
trouble, we will take a look
cheers
Bruce
On Thu, 23 Jul 2015, Tripathy, Kalyan wrote:
Hi Ani,
Thank you so much for your reply. In response to your questions:
- This is an error I have been seeing fairly frequently in a subset of my
scans, though it varies in its extent.
- It seems to be fairly consistently scattered throughout frontal cortex.
- I made a couple of correction attempts, and it seemed like being more
conservative about control point placement reduced the WM surface error but
sometimes limited my ability to successfully correct the pial surface. Is
there anything I can do to push out the pial surface in areas where I don't
see obvious WM errors?
- I haven't yet tried adding voxels to the WM instead of using control
points, and can attempt to do that next. Unlike designating a handful of
control points however, this approach will require me to individually add
every WM voxel in every frame, right?
Also, is it not possible then to combine corrected pial surfaces with the
original WM surfaces?
Thank you,
Kalyan
____________________________________________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ani Varjabedian
<a...@nmr.mgh.harvard.edu>
Sent: Thursday, July 23, 2015 8:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Question about pial surface correction through
Freesurfer
Hello Kalyan,
A few questions:
-Is this an error you see frequently in your scans, or just a one-off type
of error?
-Is it always in the same places anatomically?
-Did you make sure to put the control points in areas that were 100% white
matter, and that had intensity values < 110 ? If you put cps in a partially
volumed voxel or an area of gray matter, you will definitely mess up the
white surfs.
- Have you tried editing the wm.mgz to add voxels and push the pial surface
out? Oftentimes the wm.mgz is more forgiving (so if you add voxels to it, it
won't necessarily mess up your wm surface)
Thank you,
Ani
On 07/21/2015 05:45 PM, Tripathy, Kalyan wrote:
Hi,
I am trying to manually correct some segmentation errors through
Freesurfer. In particular, I have noticed a number of areas
where the pial surface appears to miscalculated and is excluding
chunks of grey matter. I tried using control points to push the
pial surface out, and this helped reduce the grey matter
exclusion, but now there are many places where the white matter
surface has been reconstructed too far out, such that it
includes a bunch of true grey matter within the white matter
territory.
Is there a way that I can combine the original white matter
surfaces with the corrected pial surfaces? When I tried to
combine them in this manner and run recon-all, I received an
error suggesting that the surfaces needed to match. Did I
interpret that right, and is there a way around this?
Also, do you have any recommendations as to how I can extend the
pial surface to correct grey matter omissions without incurring
new errors as a result of the correction method?
Thank you for your time and help.
Kalyan
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