Hi Julia,

I usually remove the voxels from brainmaks.mgz for the pial edits but also from wm.mgz. If you deselect the button of the pial surface in tkmedit, you will see that the white matter surface is coincident with the pial, so you also need to correct that volume. With wm.mgz as auxiliary volume you can erase the voxels from both volumes at the same time, you only need to change the brush definitions in Tools -> Configure brush info -> target main and aux volume. Don't forget to change back this definition if you want to make more corrections to only one volume.

After this I run recon-all -autorecon2-wm -autorecon3.

Cheers,
Andreia




Citando Julia Hill <julia.hill@neura.edu.au>:

Good morning,

I have a question about editing of the pial.  I have noticed that on every single scan (so well over 100), the optic nerve has been included as pial matter (see attached screenshot).  This occurs from between 5 and 10 slices in length.  Will i need to remove the voxels from every scan, and do a recon-all autorecon2-pial? 

Thank you kindly in advance,

Julia Hill

Julia Hill
Research Assistant

School of Psychiatry

University of New South Wales

Previously Prince of Wales Medical Research Institute

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