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#!/bin/bash
echo "Usage: \n sh weightedaverage.sh \"Faces*tiff\" \n "
count=9
for x in `ls -tr $1 `
do
count=`expr $count + 1` # Increment the counter
echo " count is $count and file is $x at it $i "
ANTS 2 -m PR[ template.nii,$x,1,8,-0.9 ] -t SyN[ 3 ] -r Gauss[ 3,1.5 ] -o ROBU{$count} -i 22x21x10 --MI-option 16x8000 #-a InitAffine.txt --continue-affine 0
WarpImageMultiTransform 2 $x ROBU{$count}{$i}registered.nii ROBU{$count}Warp.nii ROBU{$count}Affine.txt
ComposeMultiTransform 2 ROBU{$count}Warp.nii -R template.nii ROBU{$count}Warp.nii ROBU{$count}Affine.txt
ComposeMaps 2 ROBU{$count}Warp.nii ROBU{$count}Affine.txt ROBU{$count}Warp.nii 2
ConvertToJpg ROBU{$count}{$i}registered.nii ROBU{$count}{$i}registered.jpg
MeasureImageSimilarity 2 2 template.nii ROBU{$count}{$i}registered.nii metriclog.txt
done
# end loop
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