Dear FSL experts,
I ran free water elimination (FWE) on DTI data. SO, there are voxels with 0 intensity in FA maps (e.g. ventricles). I don't want tbss_1 to erode non-zero voxel around zero voxle on the kernel. By inspiration from Prof Smith's answer in this link https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1301&L=FSL&D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=221509 I changed tbss_1 in the following way to keep original FA image from FWE code. I wonder if it's right to do so? Many thanks in advance!
$FSLDIR/bin/fslmaths $f -min 1 -ero -roi 1 $X 1 $Y 1 $Z 0 1 FA/${f}_FA
to
$FSLDIR/bin/fslmaths $f -min 1 -roi 1 $X 1 $Y 1 $Z 0 1 FA/${f}_FA
bw,
Joyce
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