Delete cmore_applyWarp.sh

OB_pipeline/cmore_applyWarp.sh

-#!/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