if the FLAIR is reasonably high resolution (no voxel dimension greater
than around 1.5mm) then you can use the -flairpial switch to recon-all
cheers
Bruce
On Mon,
15 Jul 2013, amirhossein manzouri wrote:
Dear Bruce, Thanks again for the response. I have FLAIR images for each
subject acquired with MPRAGE/T1. I wonder in which way I can use FLAIR
images in the analyses of cortical thickness to be able to edit (subtract)
only the part of the brain which is missegmented (segmented as gray matter
where the structure is tentorium of the cerebellum) and improve
segmentation?
On Fri, Jul 12, 2013 at 6:54 PM, amirhossein manzouri
<a.h.manzo...@gmail.com> wrote:
Thanks a lot!
On Fri, Jul 12, 2013 at 4:15 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Amir
I'm not sure I understand the question. You need to
acquire them on each subject them same way you acquire
your MPRAGE/T1-weighted image. Andre van der Kouwe (ccd)
has some sequences you can use on his website if you want
guidance on parameters and such.
cheers
Bruce
On Fri, 12 Jul 2013, amirhossein manzouri wrote:
Dear Bruce,
Would you please explain how and where to
acquire FLAIR or T2 images to
solve the problem?
BR/Amir
On Thu, Jul 11, 2013 at 9:47 PM, ye tian
<tianye...@gmail.com> wrote:
Dear Bruce and Doug,
Thank you very much!
PS: I searched through my data folder and
didn't find T2 images. There
goes all my afternoon!
Ye
On Thu, Jul 11, 2013 at 1:29 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
the fix is to acquire a FLAIR or T2
image. What you are
seing is the tentorium of the cerebellum
which is very
difficult to distinguish from cortical
gray matter on a
T1-weighted image. If you don't have
either of those
datasets you probably will need to do
manual editing Bruce
On Thu, 11 Jul 2013, ye tian wrote:
Sorry!
The attachments are really showing
the same
structure, but in different
views. I have at least a hundred
slices which
include it. Since the pial
surface is not extending into
cerebellum,
should I just edit brainmask.mgz?
Is there a quicker fix to the
problem than
manual editing?
Thank you very much!
Sincerely,
Ye
On Thu, Jul 11, 2013 at 12:30 PM,
Douglas N
Greve
<gr...@nmr.mgh.harvard.edu> wrote:
what do you mean by the
structure in the
circle? The circles are
pretty big and have a lot of
WM and GM
in them.
On 07/11/2013 12:55 PM, ye
tian wrote:
Dear Doug,
Thank you very much!
Are you basically saying
that the
structure in the circle
is not part of the cortex?
Sincerely,
Ye
On Thu, Jul 11, 2013 at 11:01 AM,
Douglas N
Greve
<gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>
wrote:
yes
On 07/11/2013 11:22 AM, ye
tian wrote:
> Dear Freesurfers,
>
> Do you think I should delete
the extra
dura-like structure
in the
> attached case?
>
> Thank you very much!
>
> Sincerely,
> Ye
>
>
>
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