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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@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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