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
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ani Varjabedian
<a...@nmr.mgh.harvard.edu>
*Sent:* Tuesday, June 7, 2016 5:45:43 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Brainmask edit error
Hi Sabrina,
Jus
edu>
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 filling in the hole to see if that might help
things. If we can get the wm surf
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
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
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
>>>
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: [Freesurfe
<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 subje
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
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 mje.m...@gmail.com 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
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
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
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
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
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 subjid
and it
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
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
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
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.
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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