Hi,
On 23 Mar 2007, at 12:32, Bea Sneller wrote:
> 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).
Is C in perfect alignment to 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?
I think the only difference is that BET makes sure that the output
brain image only has positive values, scaled safely within the
current datatype. So IF the original data goes negative, then BET
clamps the output values to lie in the 2%-98% histogram range, then
rescales them to lie from 0 to just under the datatype max.
Cheers, Steve.
>
> Thanks for any help anyone can give
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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