I see. Yes, that kind of thing is hard. YOu can try the gcuts
skullstripping, which is more aggressive and can sometimes get rid of
this kind of thing, but it also is more likely to strip brain. Or
manually remove those voxels in the brainmask.mgz
cheers
Bruce
On Thu, 22 Jun 2017, Lisa
Delal
Hi Bruce,
Thank you very much for your mail. I am going to specify my question.
In fact, we saw a problem after the recon-all step. The dura was included
in the lh.pial and rh.pial. Indeed, the red demarcation included the
meninges.
I send you an attachment
Cheers
Marine
2017-06-21 18:51
Hi Marine
the brainmask is just a rough estimate of what is brain and what is not.
You don't need to worry if it is not accurate *unless* the lh.pial and/or
rh.pial surfaces end up not being accurate because of dura left in the
brainmask.
cheers
Bruce
On Wed, 21 Jun 2017, Lisa Delalande wrot
Hi,
I am a PhD student and faced a problem with Freesurfer, more specially with
segmentation. First of all, I did a typical qsub command. However, when I
cheked with tkmedit, I saw problems of brainsmask. Indeed, meninges are
often considered as grey matter.
I tried these different commands :
