nope, I would use Left-non-WM-hypointensities and
Right-non-WM-hypointensities
On Sun, 3 Sep 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you. I looked at the LookUpTable.txt for GM and I couldn't find any. I
only found labels for
Right Lesion, Left lesion, WM lesions (wmsa and other_wmsa). What does wmsa
mean and which of these
should I use as GM lesion?
Best,
Paul
On Sun, Sep 3, 2017 at 12:45 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
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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