Dear Louis, Thanks for your helpful suggestions. I will try. All the best. 2013-12-04
Rujing Zha 发件人：Louis Nicholas Vinke <vi...@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"<charujing...@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 <vi...@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"<charujing...@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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it i > s > addressed. If you believe this e-mail was sent to you in error and the e-ma > il > contains patient information, please contact the Partners Compliance HelpLi > ne at > http://www.partners.org/complianceline . If the e-mail was sent to you in e > rror > but does not contain patient information, please contact the sender and pro > perly > dispose of the e-mail. > > >
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