Hi,
You can load up the BET mask that you currently have in fslview and overlay it on top of your original image. You can do it all through point and click in the GUI, but you can do it quickly from the command line:

fslview IMAGE IMAGE_brain_mask -l Red -t 0.8

This will overlay the brainmask in Red with a transparency value of 0.8. Once in fslview, unlock the image, make your edits with the pen tool, and then save your edited brainmask.

Good luck,
Niels

On Mon, Oct 6, 2014 at 11:22 AM, Frederik <[log in to unmask]> wrote:
hello all,
I tried out the manual Mask-creating tool and have to say that it does not solve my problem unfortunately.
I would have to create a mask that contains the whole brain plus the optical nerve slice for slice with the pen and that would take way too long if I had to apply that to every subject. What I need is a possibility to edit the * _brain_mask.nii.gz that I receive out of BET. Anyway thank you a lot for the good first thought on my problem :) Any further ideas maybe? I'm glad for every tip!
Best regards,
Frederik



--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
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