Hi Linn
it looks like a hypo intense region surrounded by a hyper-intense one, no?
I think if you edit those voxels in the aseg.mgz to be "white matter
hypointensities" or "lesion" then run the recon from there forward it
should be ok
Bruce
On Mon, 3 Feb 2014, Linn Christin Bonaventure Norbom wrote:
---------- Forwarded message ----------
From: Linn Christin Bonaventure Norbom <linnnor...@gmail.com>
Date: Mon, Feb 3, 2014 at 5:44 PM
Subject: Re: [Freesurfer] Difficulties with including hypo-intense areas
(MS-lesions) as white matter without additionally transforming the lesion
into "normal white matter".
To: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Hi again,
Sorry for being unclear.
Here is a picture of the lesion. If I understand correctly it is now NOT
included as white matter. All I want to do is include it as white matter, so
that it will be registered as a hypo-intense area in aseg.stats.
So the way to do this is to edit the aseg.mgz and not the wm.mgz?
Cheers
Linn Norbom
On Mon, Feb 3, 2014 at 5:30 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Linn
I'm not sure I understand, but if you can paste them into the
aseg.mgz as hypointensities I think things should work properly
cheers
Bruce
On Mon, 3 Feb 2014, Linn Christin Bonaventure Norbom wrote:
Hi,
I would like to include unregistered hypo-intense
lesions into white matter
(as now they are excluded from cortex, and not
registered as anything)
without transforming the lesion from hypo-intense to
normal (110). Is it
possible to include these areas in white matter
and additionally keep the
statistic volume of these areas as hypo-intense-wm
in the aseg.stats?
Thank you in advance,
Regards Linn Norbom
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