Commit 73739900 authored by Christoph Arthofer's avatar Christoph Arthofer
Browse files

Delete cmore_applyWarp.sh

parent f0f29d28
#!/bin/bash
#$ -cwd -j y
#$ -r y
echo `date`: Executing task ${SGE_TASK_ID} of job ${JOB_ID} on `hostname` as user ${USER}
echo SGE_TASK_FIRST=${SGE_TASK_FIRST}, SGE_TASK_LAST=${SGE_TASK_LAST}, SGE_TASK_STEPSIZE=${SGE_TASK_STEPSIZE}
. ~/.bash_profile
. $MODULESHOME/init/bash
module load fsl/6.0.3
ID_PATH=$1
IMG_PATH=$2
WARP_PATH=$3
WARPED_IMG_PATH=$4
WARPED_IMG_NORM_PATH=$5
PREMAT_PATH=$6
REF_PATH=$7
IMG_IN_ID=$(awk 'NR=='${SGE_TASK_ID} ${ID_PATH})
echo ${IMG_IN_ID}
printf -v IMG_PATH ${IMG_PATH} $((10#$IMG_IN_ID))
printf -v WARP_PATH ${WARP_PATH} $((10#$IMG_IN_ID))
printf -v WARPED_IMG_PATH ${WARPED_IMG_PATH} $((10#$IMG_IN_ID))
printf -v WARPED_IMG_NORM_PATH ${WARPED_IMG_NORM_PATH} $((10#$IMG_IN_ID))
printf -v PREMAT_PATH ${PREMAT_PATH} $((10#$IMG_IN_ID))
echo "applywarp -i ${IMG_PATH} -o ${WARPED_IMG_PATH} -r ${REF_PATH} -w ${WARP_PATH} --premat=${PREMAT_PATH} --interp=spline -v"
applywarp -i ${IMG_PATH} -o ${WARPED_IMG_PATH} -r ${REF_PATH} -w ${WARP_PATH} --premat=${PREMAT_PATH} --interp=spline -v
fslmaths ${WARPED_IMG_PATH} -inm 1000 ${WARPED_IMG_NORM_PATH}
rv=$?
echo `date`: task complete
exit $rv
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