Hi Paul
GM ones are harder and I'm not sure we have a working procedure for them
yet. I think we have separate labels for wm and gm lesions - try using them
when you edit the aseg.
cheers
Bruce
On Sun, 3 Sep 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you very much. I'm guessing I should follow the tutorial for
editing aseg; or is there a different tutorial on how to edit and label
WM lesions on aseg? One last question, what if it's a combination of WM
and GM lesions like cortical stroke that extended into the WM? Should I
use the same procedure?
Best,
Paul
Sent from my BlackBerry 10 smartphone.
Original Message
From: Bruce Fischl
Sent: Sunday, September 3, 2017 11:47 AM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer with infarct patients
Hi Paul
if they are WM lesions I think you should edit the aseg and label them as
such, then run from there forward. It should propagate the lesions from
aseg to wm.mgz, so you shouldn't have to do both
Bruce
On Sun, 3 Sep 2017, miracle ozzoude wrote:
Hello Bruce,
I am interested in this thread because I have encountered similar problems with
my stroke patients.
How do I solve it? Should I only edit the aseg and assign a label called
"Lesion" in the FS
LookUpTable? or Should I edit both the wm.mgz and aseg.mgz files? If the
former, How do I achieve
it? My goal is to make sure that WH and GM surfaces are traced properly. Any
help will be
appreciated. Thank you.
Best,
Paul
On Wed, Jun 21, 2017 at 12:45 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Mariana
yes, control points would mess everything up. It looks like the rest of the
surface was
generated pretty accurately though - do you need to correct anything?
cheers
Bruce
On Wed, 21 Jun 2017, Budge, Mariana wrote:
Hi Freesurfer experts,
I am running FS on a patient with a chronic right occipital lobe infarct as
part of a larger study. The program does not recognize the area around the
lesion as brain matter, and I am wondering how best to treat this situation.
I am worried that adding Control Points will incorrectly label the region as
white matter. I am attaching some pictures of slices where this is apparent.
Thank you so much for your help!
Best,
Mariana
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