Hi again, I realize my last question about the brainmask did not make sense. I meant to ask if I have to either manually delete all non-brain voxels around the eye area which is very time consuming per subject or just delete those misclassified as GM? ( I check this through this command: tkmedit subj_output brainmask.mgz -aux T1.mgz -surfs)
Also for some subjects: 1. When I open freeview and look at the aseg file there is area around the eye misclassified as cerebral cortex for some subjects. 2. When I load the pial surface the aseg file shows cerebral cortex in the temporal poles and frontal lobes near the eye region outside of the pial surface outline. How do I edit this? I look forward to your response. Thanks. On Tue, Dec 12, 2017 at 4:21 PM, FSL Analysis <fslanaly...@gmail.com> wrote: > Hi all, > > I have processed data using freesurfer and the output for most of my > subjects did not remove all of the eye and dura around it during skull > stripping. When I check the brainmask there is dura (or blood vessel) in > the frontal lobe that is classified as GM. > > I am wondering if I have to manually edit the skullstrip and rerun > recon-all or do I just edit the brainmask file by deleting non-brain > voxels? Or do I have to do both? > > If I only edit the brainmask file does this skip any other important > processing steps that may affect my results? > > I am planning on looking at brain volumes and cortical thickness and how > they relate to behavioral measures. > > > > > Kind Regards, > > Ciara >
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