# output: ${T1}_biascorr [ other intermediates to be cleaned up ]
if[$do_biasrestore=yes];then
if[$strongbias=yes];then
date;echo"Estimating and removing field (stage 1 - large-scale fields)"
# for the first step (very gross bias field) don't worry about the lesionmask
# the following is a replacement for : run $FSLDIR/bin/fslmaths ${T1} -s 20 ${T1}_s20
quick_smooth ${T1}${T1}_s20
run $FSLDIR/bin/fslmaths ${T1}-div${T1}_s20 ${T1}_hpf
if[$do_bet=yes];then
date;echo"Estimating and removing field (stage 1 - large-scale fields)"
# for the first step (very gross bias field) don't worry about the lesionmask
# the following is a replacement for : run $FSLDIR/bin/fslmaths ${T1} -s 20 ${T1}_s20
quick_smooth ${T1}${T1}_s20
run $FSLDIR/bin/fslmaths ${T1}-div${T1}_s20 ${T1}_hpf
if[$do_bet=yes];then
# get a rough brain mask - it can be *VERY* rough (i.e. missing huge portions of the brain or including non-brain, but non-background) - use -f 0.1 to err on being over inclusive
run $FSLDIR/bin/bet ${T1}_hpf ${T1}_hpf_brain -m-f 0.1
else
run $FSLDIR/bin/fslmaths ${T1}_hpf ${T1}_hpf_brain
run $FSLDIR/bin/fslmaths ${T1}_hpf_brain -bin${T1}_hpf_brain_mask
fi
run $FSLDIR/bin/fslmaths ${T1}_hpf_brain_mask -mas lesionmaskinv ${T1}_hpf_brain_mask
run $FSLDIR/bin/bet ${T1}_hpf ${T1}_hpf_brain -m-f 0.1
else
run $FSLDIR/bin/fslmaths ${T1}_hpf ${T1}_hpf_brain
run $FSLDIR/bin/fslmaths ${T1}_hpf_brain -bin${T1}_hpf_brain_mask
fi
run $FSLDIR/bin/fslmaths ${T1}_hpf_brain_mask -mas lesionmaskinv ${T1}_hpf_brain_mask
# get a smoothed version without the edge effects
run $FSLDIR/bin/fslmaths ${T1}-mas${T1}_hpf_brain_mask ${T1}_hpf_s20
run $FSLDIR/bin/fslmaths ${T1}_hpf2_brain -div$med1-mul$med0${T1}_hpf2_brain
date;echo"Estimating and removing bias field (stage 2 - detailed fields)"
run $FSLDIR/bin/fslmaths ${T1}_hpf2_brain -mas lesionmaskinv ${T1}_hpf2_maskedbrain
run $FSLDIR/bin/fast -o${T1}_initfast -l${smooth}-b-B-t$type--iter=${niter}--nopve--fixed=0 -v${T1}_hpf2_maskedbrain
run $FSLDIR/bin/fslmaths ${T1}_initfast_restore -mas lesionmaskinv ${T1}_initfast_maskedrestore
run $FSLDIR/bin/fast -o${T1}_initfast2 -l${smooth}-b-B-t$type--iter=${niter}--nopve--fixed=0 -v${T1}_initfast_maskedrestore
run $FSLDIR/bin/fslmaths ${T1}_hpf_brain_mask ${T1}_initfast2_brain_mask
else
if[$do_bet=yes];then
if[$do_bet=yes];then
# get a rough brain mask - it can be *VERY* rough (i.e. missing huge portions of the brain or including non-brain, but non-background) - use -f 0.1 to err on being over inclusive
run $FSLDIR/bin/bet ${T1}${T1}_initfast2_brain -m-f 0.1
else
run $FSLDIR/bin/fslmaths ${T1}${T1}_initfast2_brain
run $FSLDIR/bin/fslmaths ${T1}_initfast2_brain -bin${T1}_initfast2_brain_mask
fi
run $FSLDIR/bin/fslmaths ${T1}_initfast2_brain ${T1}_initfast2_restore
run $FSLDIR/bin/bet ${T1}${T1}_initfast2_brain -m-f 0.1
else
run $FSLDIR/bin/fslmaths ${T1}${T1}_initfast2_brain
run $FSLDIR/bin/fslmaths ${T1}_initfast2_brain -bin${T1}_initfast2_brain_mask
fi
run $FSLDIR/bin/fslmaths ${T1}_initfast2_brain ${T1}_initfast2_restore
fi
# redo fast again to try and improve bias field
run $FSLDIR/bin/fslmaths ${T1}_initfast2_restore -mas lesionmaskinv ${T1}_initfast2_maskedrestore