fill_nw

#!/bin/sh

Usage() {
    cat <<EOF
fill_nw - Fills enclosed portions of a mask. Iteratively dilates and masks until convergence.

For research purposes only! Please see LICENSE.txt

Nate Wetter <nwetter2@illinois.edu>
Brad Sutton <bsutton@illinois.edu>
Magnetic Resonance Functional Imaging Lab <mrfil.bioen.illinois.edu>
University of Illinois at Urbana-Champaign <illinois.edu>

Use: fill_nw <in> <mask> <out>

Required parameters:
  <in>   : Input image to be dilated.
  <mask> : Mask with enclosed portions to be filled. Masks <in> every iteration.
  <out>  : Output file name.

Last updated: September 24, 2014

EOF
    exit 1
}

[ -z "$3" ] && Usage

in=`remove_ext $1`
mask=`remove_ext $2`
out=`remove_ext $3`
failed=0

# verify validity of input images
if [ `imtest $in` = 0 ]; then
    echo "ERROR: $in (input image) is not a valid image"
    failed=1
fi
if [ `imtest $mask` = 0 ]; then
    echo "ERROR: $mask (mask image) is not a valid image"
    failed=1
fi
if [ "$failed" = 1 ]; then
    echo "Exiting"
    exit 1
fi

# begin computation
cluster --in=${mask} --thresh=0.5 -o ${mask}_cluster --no_table
index_max=$(fslstats ${mask}_cluster -R | cut -d' ' -f2 | cut -d'.' -f1)
index_cur=1
while [ $index_cur -le $index_max ]
do
    echo $index_cur
    index_prev=`expr $index_cur - 1`

    fslmaths ${mask}_cluster -thr ${index_prev}.5 -uthr ${index_cur}.5 cluster_current
    fslmaths cluster_current -mas $in cluster_current_masked
    if [ $(fslstats cluster_current_masked -R | cut -d' ' -f2 | cut -d'.' -f1) -eq 0 ]; then
        # remove cluster
        #fslmaths cluster_current -binv cluster_current_inv
        #fslmaths ${mask}_cluster -mas cluster_current_inv ${mask}_cluster
        fslmaths ${mask}_cluster -sub cluster_current ${mask}_cluster
        echo "cluster rejected $(fslstats cluster_current -R | cut -d' ' -f2 | cut -d'.' -f1) = $index_cur"
    else
        echo "cluster retained"
    fi
    index_cur=`expr $index_cur + 1`
done
immv ${mask}_cluster $out