Hi Rachel,
This appears to be some kind of openGL rendering artifact that we are
not able to reproduce nor find a definitive solution, unfortunately. It
happened to some of us over the years but very very rarely and we were
never able to replicate it. It may be a hardware/system glitch. Would
what is your freeview command?
On 6/14/17 3:51 PM, KALEY E ELLIS wrote:
Dear FreeSurfer Developers,
We are using FreeSurfer v6.0 and our operating system is OS X El
Capitan version 10.11.6.
We are going through the manual editing process and are checking the
brainmask by following these
-
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Ani Varjabedian
*Sent:* Tuesday, June 7, 2016 5:45:43 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Brainmask edit error
Hi Sabrina,
Just wanted to update you on my progress.
I tried editing the wm.mgz and fill
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Brainmask edit error
Hi Sabrina,
Just wanted to update you on my progress.
I tried editing the wm.mgz and filling in the hole to see if that might help
things. If we can get the wm surface accurate then there is a good chance the
pial surf (which grows from the white
instead of trying to edit the surfaces?
Thank you,
Sabrina
From:freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
Sent: Monday, May 23, 2016 12:30:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Brainmask edit error
because it
tion. 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 try
eview instead of trying to edit the surfaces?
Thank you,
Sabrina
From:freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
Sent: Monday, May 23, 2016 12:30:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Brainmask edit error
bec
edit the surfaces?
>>>
>>> Thank you,
>>> Sabrina
>>> ____
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> on behalf of Bruce Fischl
>>>
>>> Sent: Monday, May 23, 2016 12:30:30 PM
>
label file
in freeview instead of trying to edit the surfaces?
Thank you,
Sabrina
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
Sent: Monday, May 23, 2016 12:30:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Brainmask
you,
Sabrina
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
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
y not be possible to get good surfaces with
> extensive strokes?
>
> Thank you,
> Sabrina
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Bruce Fischl
>
> Sent: Thursday, May 19, 2016 11:24:51 AM
> To:
on behalf of Bruce Fischl
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 sur
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 s
Are you sure? Did you flip back and forth between this and a volume with the
skull?
> On Aug 25, 2014, at 7:13 AM, Mads Jensen wrote:
>
> Hi Bruce (and the rest of the list),
>
> It looks better (see attached) but it still look like it removed too much.
>
> cheers for the point though,
> Mads
Hi Bruce (and the rest of the list),
It looks better (see attached) but it still look like it removed too much.
cheers for the point though,
Mads
On 21/08/14 16:22, Bruce Fischl wrote:
Hi Mads
what does it look like if you move off the mideline? Or check a coronal
view? Sagittal views of the
Hi Mads
what does it look like if you move off the mideline? Or check a coronal
view? Sagittal views of the midline are notoriously bad for judging skull
stripping accuracy
cheers
Bruce
On Tue, 19 Aug 2014, Mads Jensen wrote:
> Dear list,
>
> I have problem with the brainmask from a subject wh
Question regarding the use of skull stripping errors. I am wondering if it is
possible to correct (use the -wsthresh or -gcut) in longitudinal processed data
or would these types of edits be required in the earlier processing steps
(initial FreeSurfer recon-all)?
Thanks in advance for any help
Hi Elisa
it's tough to tell from just the wm.mgz image. Are the voxels excluded
from the pial brain or are they dura? What does the orig surface show? If
the orig doesn't follow the wm.mgz and you think it should, that means
there is a topological defect that was inaccurately corrected and you
Yes, you would just run the command for the fix that happens earliest on
in the processing stream. The order these fixes occur in the processing
stream is:
control points
wm edits
pial edits
So if you've done all 3, you only need to run
recon-all -autorecon2-cp -autorecon3 -s
and it will take
Hello all,
I am new to FreeSurfer and still trying to understand how things work.
I am currently trying to understand how the manual correction works.
Following the online tutorials I was able to fix the brainmask and
wm.mgz, and also add control points in the wm so that low intensity wm
is also
Hi Helen,
That's a good question. You don't have to start at autorecon1, however.
When you run -autorecon2-wm or -autorecon2-pial one of the first steps is:
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
which is changing the brain.finalsurfs.mgz to take into account the
changes yo
Hi,
I have a similar questionto the one listed below.
After I edit brainmask.mgz and wm.mgz, my understanding was that I could
run
autorecon2-wm
and would not have to run autorecon2-pial because -wm will run
everything else through the end of -autorecon2.
However, if brainmask.mgz is run at th
aparc+aseg.mgz is probably better. See
surfer.nmr.mgh.harvard.edu/fswiki/BrainVolume for the answer to your
question.
Satrajit Ghosh wrote:
> if one wants to get at the brain only (similar to bet), is
> brainmask.mgz the best file to use? on some of our data, we are
> noticing a lot of eyeball
if one wants to get at the brain only (similar to bet), is brainmask.mgz the
best file to use? on some of our data, we are noticing a lot of eyeball.
i presume one can use aseg as an alternative. is this more recommended than
brainmask.mgz? also, is the total brain volume computation based on aseg
Hi,
I am running FS-4.3.0 and after recon-all -all, I am finding in aseg.stats of
quite a few of my subjects that brain mask volume (1735600 mm^3) is greater
than ICV (1701891 mm^3).
The talairach failure detection passed fine: talairach.xfm OK (p=0.7556,
pval=0.6675 >= threshold 0.005 ).
The
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