Hi Sabrina,
I'm not entirely sure about that, but if my manual edits don't work I'll
let Bruce know and we can discuss other workarounds.
-Ani
On 06/02/2016 12:55 PM, Sabrina Yu wrote:
Hi Ani,
Thanks so much for your explanation, it makes sense that the brain is
too deformed for one continuous surface. If we are not able to find a
workaround that creates a continuous surface, can I create a separate
surface just for the stroke region? And generate average voxel
intensity for that region?
Thanks,
Sabrina
On Jun 2, 2016, at 6:21 PM, Ani Varjabedian <a...@nmr.mgh.harvard.edu
<mailto:a...@nmr.mgh.harvard.edu>> wrote:
Hi Sabrina,
Usually we don't add voxels in the brainmask. We usually add to the
wm.mgz which pushes the white surf out and ultimately the pial surf
out (because it grows from the white).
If the area around the stroke on both sides looks good but there is a
hole in the middle where there is no information or labels, then the
surfaces will not connect all the way around it. They treat it like
two separate pieces. Does this make sense? I'll try to play around
with some different things (like adding to the wm.mgz) and see if I
can get the surfaces to be continuous around this region.
Like Bruce said, it might end up being that the brain is too
different from what freesurfer assumes a brain to look like, but I
will try some work arounds and get back to you.
Thank you,
Ani
On 06/02/2016 08:18 AM, Sabrina Yu wrote:
Hi Ani,
Thanks for looking into this for me. I'm actually out of town right
now, so cannot access the subject in front of me.
Yes, it is. As I am trying to generate the stats on intensity over
an ROI, I am hoping to be able to generate good surfaces. To me, the
aseg looks pretty good. The brain matter around the stroke area is
recognized, but is not in the surfaces.
I only edited the brainmask.mgz. I unfortunately cannot tell you the
exact slices that I edited until I am back, but I tried to recon
edit and add in voxels in the stroke area. I did not notice major
problems with the surface including dura or skull, so I did not
really remove voxels. I'm not sure if how I did it is correct, but I
tried to follow the wiki page on pial surface edits. The command I
used to try to regenerate the surface was: recon-all -subjid
<SUBJECT> -autorecon2-pial
Thanks,
Sabrina
On Jun 1, 2016, at 4:39 PM, Ani Varjabedian
<a...@nmr.mgh.harvard.edu> wrote:
Hello Sabrina,
I have received the subject and am looking at it now.
I've attached a screenshot that is similar to the one you sent. At
[158, 115, 124] I see a hole in the aseg, wm mask, so it makes
sense that the brainmask does not cross over the area. Is this the
area you wish to include? I just want to make sure I'm looking at
the correct region.
What have you done so far to edit? I know you mentioned brainmask
editing, but what specifically did you do?
Thank you,
Ani
On 05/25/2016 08:47 AM, Ani Varjabedian wrote:
Hi Sabrina,
Could you upload the whole subject folder to the FTP or to our
filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2/
I can play around with the data a bit to see if we can improve
surfaces. If that doesn't work then we can discuss other options
for how to get the information you need.
Thanks!
-Ani
On 05/23/2016 05:47 PM, Sabrina Yu wrote:
Thank you for your explanation. Would it be possible to find a workaround? I
want to generate stats on intensity over an ROI for these stroke subjects. For
the brain matter not included in the surface, can I create a volume label file
in freeview instead of trying to edit the surfaces?
Thank you,
Sabrina
________________________________________
From:freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Bruce Fischl<fis...@nmr.mgh.harvard.edu>
Sent: Monday, May 23, 2016 12:30:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Brainmask edit error
because it violates too many of our assumptions about the topology and
geometry of the brain.
cheers
Bruce
On Mon, 23 May 2016, Sabrina Yu
wrote:
Hi Bruce,
Thank you for your reply. I've uploaded the .mgz and surfaces using FTP to
FreeSurfer. Why is it that it may not be possible to get good surfaces with
extensive strokes?
Thank you,
Sabrina
________________________________________
From:freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Bruce Fischl<fis...@nmr.mgh.harvard.edu>
Sent: Thursday, May 19, 2016 11:24:51 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Brainmask edit error
Hi Sabrina
it's tough to tell from just the 2 slices. If you upload the subject one
of us will take a look, but it may not be possible to get good surfaces
with that extensive a stroke
cheers
Bruce
On Wed, 18 May 2016, Sabrina Yu wrote:
Hello,
I'm having problems with regenerating the surfaces for stroke cases after
editing the brainmask.mgz file. In the aseg.mgz file, the brain matter
around lesion area is correctly classified as brain matter. In the pial
surface, this brain matter is not included.
I've tried to edit the brainmask.mgz file to include this region, but when I
run: recon-all -subjid <SUBJECT> -autorecon2-pial, the surfaces generated
are not changed at all.
I have attached some images to this email. I'm new to Freesurfer, so any
help would be greatly appreciated.
Thank you.
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The information in this e-mail is intended only for the person to
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the e-mail
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the e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
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you in error
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and properly
dispose of the e-mail.
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