yes, I think so. It may not work for the GM ones at the moment, but should at least be fixable
On Sun, 3 Sep 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you very much. To reiterate our discussion, I should use Left/Right non-WM-hypointensities for
GM lesions and Left/Right-WM-hypointensities for WM lesions when editing the aseg.presurf.mgz.
Correct?
Best,
Paul
On Sun, Sep 3, 2017 at 1:52 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
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 <fischl@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
<fischl@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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