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 <fslanalysis@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