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#! /bin/bash
ANTSPATH=$1
if [ ${#ANTSPATH} -lt 3 ] ; then
echo usage
echo $0 PATH_TO_ANTS_BINARIES image_to_label.nii.gz
exit
fi
if ! command -v ants.sh &> /dev/null
then
echo you need the file ants.sh - exiting
exit
fi
Image_To_Be_Labeled=$2
if [[ ! -s $Image_To_Be_Labeled ]] || [[ ${#Image_To_Be_Labeled} -lt 3 ]] ; then
echo you need to pass an image you want to label as the 2nd argument
echo " you tried to pass $Image_To_Be_Labeled with name length ${#Image_To_Be_Labeled} --- sure that's right? "
exit
fi
LONGITERATIONS=30x50x30
FASTITERATIONS=10x0x0
ct=0
LIST_OF_IMAGES=" image1.nii.gz image2.nii.gz "
LIST_OF_LABELS=( image1_labels.nii.gz image2_labels.nii.gz )
LIST_OF_OUTPUT=( image1_output image2_output )
for labeled_img in $LIST_OF_IMAGES ; do
sh ants.sh 3 $labeled_img $Image_To_Be_Labeled ${LIST_OF_OUTPUT[${ct}]} $FASTITERATIONS ${LIST_OF_LABELS[${ct}]}
let ct=$ct+1
done
ls *labeled.nii.gz > labeled_list.txt
ImageSetStatistics 3 labeled_list.txt new_subject_labels.nii.gz 1
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