You could:
1) Draw your mask of the bit of skull you want to remove
2) Use avwmaths++ <mask> -sub 1 -mul -1 <outputmask> to covert the mask to
the inverse (all voxels outside the mask become negative 1 while the mask
becomes zero, then multiply by negative 1 to reverse the signs.
3) Use avwmaths++ -mas as normal.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Jennifer Townsend
Sent: Monday, July 16, 2007 6:27 PM
To: [log in to unmask]
Subject: [FSL] avwmaths- exclusive mask
I ran into a problem skull stripping and after removing bottom/neck slices,
recentering the image and playing with the -f and -g options, I still get a
bit of skull at the top. I'd like to manual remove this using an exclusive
mask of the unwanted skull bits. avwmaths -mas is an inclusive masking. Is
there a way to do the reverse of this? I tried using -sub, but it only
excludes the outer background part of my mask and leaves in the skull part.
Any suggestions short of manually drawing the brain for all 130 slices?
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