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
------------------------------------------------------------------------
The materials in this message are private and may contain Protected
Healthcare Information or other information of a sensitive nature. If
you are not the intended recipient, be advised that any unauthorized
use, disclosure, copying or the taking of any action in reliance on
the contents of this information is strictly prohibited. If you have
received this email in error, please immediately notify the sender via
telephone or return mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.