you could I guess, but it will likely be hard, a lot of work, and not that
repeatable
cheers
Bruce
On Sat, 2 May 2020, Zeng, Victor (BIDMC - Keshavan -
Psychiatry) wrote:
Hi all,
I was doing a little bit more researching. Could you just fix this sort of
issue by editing the aparc.auto.mgz and changing the label from
Left/Right-Cerebral-White-Matter to Left/Right-Cerebral-Cortex as necessary?
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
________________________________________
From: Zeng,Victor (BIDMC - Keshavan - Psychiatry)
Sent: Sunday, April 26, 2020 7:28 PM
To: Freesurfer support list
Subject: Re: [External] Re: [Freesurfer] Intensity inhomogeneity messing with
the wm.mgz
Hi,
Thanks for the clarification. From my understanding, control points are used to
grab regions that should be white matter, rather than remove regions that
aren't white matter. Are there any resources on how you would use control
points to remove intensity inhomogeneity?
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Sent: Sunday, April 26, 2020 12:03 PM
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] Intensity inhomogeneity messing with the
wm.mgz
Hi Victor
the best way to remove intensity inhomogeneities is with control points
usually. The wm.mgz gives us an initial estimate of the surface locations,
but we then deform it based on the intensities in the brain.mgz volume. So
if it looks like wm extends that far out in the brain your wm.mgz edits are
unliekly to fix things
cheers
Bruce
On Sun, 26 Apr 2020, Zeng, Victor (BIDMC - Keshavan -
Psychiatry)
wrote:
Hi Freesurfer developers,
I have a subsample of a FS dataset that have scanner-originated
hyperintensities in the bilateral
supramarginal/temporal lobes. I've manually removed these hyperintensities by
editing the wm.mgz, yet FS
seems to be unable to recognize these edits when looking at the ?h.white and
aparc+aseg.mgz. Is there a
possible way to rectify these errors?
I am using FS6 for linux
Here are some pictures:
[IMAGE][IMAGE]
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
________________________________________________________________________________________________________
This message is intended for the use of the person(s) to whom it may be
addressed. It may contain
information that is privileged, confidential, or otherwise protected from
disclosure under applicable
law. If you are not the intended recipient, any dissemination, distribution,
copying, or use of this
information is prohibited. If you have received this message in error, please
permanently delete it and
immediately notify the sender. Thank you.
_______________________________________________
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
