Dear fsl experts,
I'm trying to register FA maps from two timepoints to the half space and I used the code provided below:
flirt -in t1 -ref t2 -dof 10 -omat t1-to-t2.mat
flirt -in t2 -ref t1 -dof 10 -omat t2-to-t1.mat
convert_xfm -omat inv_t1_to_t2.mat -inverse t1-to-t2.mat
convert_xfm -omat inv_t2_to_t1.mat -inverse t2-to-t1.mat
midtrans --template=t2 -o avg-t1-to-t2.mat t2-to-t1.mat inv_t1_to_t2.mat
midtrans --template=t2 -o avg-t2-to-t1.mat t1-to-t2.mat inv_t2_to_t1.mat
midtrans --template=t1 -o t1-to-midspace.mat avg-t2-to-t1.mat ${FSLDIR}/etc/flirtsch/ident.mat
midtrans --template=t2 -o t2-to-midspace.mat avg-t1-to-t2.mat ${FSLDIR}/etc/flirtsch/ident.mat
flirt -in t1 -ref t2 -applyxfm -init t2-to-midspace.mat -o sca1_halfway -interp sinc
flirt -in t2 -ref t1 -applyxfm -init t1-to-midspace.mat -o sca2_halfway -interp sinc
fslmaths sca1_halfway -add sca2_halfway -div 2 template_halfway_space
However, when I do averaging at the last steps, I got the warning of inconsistent orientation. I can inform you that t1/t2 have identical qform/sform. I also use sinc interpolation instead of spline because spline doesnot exist for a previous version of fsl. Can anyone please let me know if I am doing something wrong?
Best
/Kami
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