Hi,
This cannot have anything to do with the space that they are in, at least not for this call to fslmaths. Have you checked that the input image, GM_merg contains sensible values in all the volumes? It might help to try it without the -bin or -odt char and see what the output values are.
All the best,
Mark
Oskar W <[log in to unmask]> wrote:
Hi all,
Why do I get an empty GM_mask when trying
$FSLDIR/bin/fslmaths GM_merg -Tmean -thr 0.01 -bin GM_mask -odt char
even though the GM_merg, in MNI space, is apparently OK?
When the GM_merg is instead in "Aligned anatomical", the problem does not occur. Why does it work then, and if so, how do I get the MNI space images to Aligned anatomical?
Cheers,
Oskar W
M.Sc. Eng.Phys.
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