I'm trying to use Siena to calculate the volumetric difference between two
images (A and B) using the brain mask from a third image (C) in place of
the brain mask from the second (B).
I have modified the siena script so that it reads in 3 images: A, B, C and
then in the extract brain section i have left the bet call for image A the
same but have modified second bet call to:
${FSLDIR}/bin/bet $C ${B}_brain -s -m -n
and then tried to apply the output mask to image B to generate ${B}_brain.
${FSLDIR}/bin/avwmaths $B -mas ${B}_brain_mask ${B}_brain
However the results that this script then produced did not seem quite
right so i then investigated the two outputs ${B}_brain
from: bet $B ${B}_brain -s -m
and from: bet $B ${B}_brain -s -m -n
avwmaths $B -mas ${B}_brain_mask ${B}_brain
and found that they were not the same. The output from just using bet
seems to be thresholded and scaled. Is this the case and if so how much
by? If not, is there a better way i can use the mask from the third image
(C) as a replacement for the mask from B?
Thanks for any help anyone can give
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