when you say there is some skull considered to be gray matter, do you
mean in the aseg or does the pial surface contain it? If it's the aseg
then it probably doesn't matter as we don't use the asegs for cortical
stuff in any case
cheers
Bruce
On Tue, 3 Dec 2013, Rujing Zha wrote:
Dear Louis,
Thanks for your helpful prompt in advance.
I see. In my case, there is a not properly stripping, there is a not
properly gray matter(there are a some skull considered as gray matter). Did
you mean I can draw the segmentation without considering the skull
stripping? And a bad brainmask.mgz will not influence the GM thickness
analysis?
Thanks in advance.
All the best.
2013-12-03
____________________________________________________________________________
Rujing Zha
____________________________________________________________________________
发件人：Louis Nicholas Vinke <[email protected]>
发送时间：2013-12-03 03:58
主题：Re: [Freesurfer] recon-all strip skull and neck by brain volume mask
收件人："Rujing Zha"<[email protected]>
抄送："freesurfer"<[email protected]>
Hi Rujing,
Even if there is some skull/dura left after the skullstrip step in
recon-all, it still may not negatively impact the surfaces. It might be
worth running the remaining recon-all steps to see how the surfaces turn
out.
If you want to swap-in a better skullstripped volume into the recon-all
stream then you just need to replace the brainmask.mgz and continue with
autorecon2 and autorecon3.
Keep in mind that the new brainmask.mgz volume still needs to be in the
conformed anatomical space, so use the T1.mgz or brainmask.mgz to create
the improved skullstrip volume which will replace the existing
brainmask.mgz.
-Louis
On Mon, 2 Dec 2013, Rujing Zha wrote:
> Dear all,
> Part of subjects 3d images cannot be stripped skull and neck properly in
?? ?> recon-all default. I have got the brain volume mask, how I can using the
?? ?> existing proper mask to help strip skull in recon-all and next workflow?
?? ?> Thanks.Any reply will be appreciated.
> All the best.
>
> 2013-12-02
>
> _________________________________________________________________________
___
> Rujing Zha
>
>
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