Hi Ciara
what version are you running? I think you only need to correct voxels that cause the white and/or pial surfaces to be incorrect, as we correct the aseg with them (at least I think we do in v6)
cheers Bruce
On Wed, 13 Dec 2017, FSL Analysis wrote:
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:
- When I open freeview and look at the aseg file there is area around the eye misclassified as cerebral cortex for some subjects.
- 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