Dear Louis, Thanks for your helpful suggestions. I will try. All the best.
2013-12-04
Rujing Zha
发件人：Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu 发送时间：2013-12-03 23:13 主题：Re: Re: [Freesurfer] recon-all strip skull and neck by brain volume mask 收件人："Rujing Zha"charujing123@163.com 抄送："freesurfer"freesurfer@nmr.mgh.harvard.edu
Hi Rujing, If portions of gray matter have been removed, then that will need to be corrected. You can definitely remove skull/dura manually from the brainmask.mgz volume (see link below), but that can be time-consuming and may not be necessary. It's hard to know for sure if a brainmask.mgz is bad until you have generated the surfaces or have some experience with similar cases processed with Freesurfer.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview
-Louis
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 vinke@nmr.mgh.harvard.edu 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"charujing123@163.com 抄送："freesurfer"freesurfer@nmr.mgh.harvard.edu
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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