Delete cmore_FLIRT_registration.sh

OB_pipeline/cmore_FLIRT_registration.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
-DATA_DIR=$2
-OUT_DIR=$3
-IMG_REF_PATH=$4
-IMG_REF_ID=$5
-
-IMG_IN_ID=$(awk 'NR=='${SGE_TASK_ID} ${ID_PATH})
-
-IMG_IN_PATH="${DATA_DIR}${IMG_IN_ID}/T1/T1_unbiased_brain.nii.gz"
-
-IMG_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_T1reg.nii.gz"
-OMAT_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_T1reg.mat"
-
-echo "flirt -in ${IMG_IN_PATH} -ref ${IMG_REF_PATH} -out ${IMG_OUT_PATH} -omat ${OMAT_OUT_PATH}"
-flirt -in ${IMG_IN_PATH} -ref ${IMG_REF_PATH} -omat ${OMAT_OUT_PATH}
-
-HEAD_IMG_IN_PATH="${DATA_DIR}${IMG_IN_ID}/T1/T1_unbiased.nii.gz"
-echo "flirt -in ${HEAD_IMG_IN_PATH} -ref ${IMG_REF_PATH} -out ${IMG_OUT_PATH} -applyxfm -init ${OMAT_OUT_PATH} -interp spline"
-flirt -in ${HEAD_IMG_IN_PATH} -ref ${IMG_REF_PATH} -out ${IMG_OUT_PATH} -applyxfm -init ${OMAT_OUT_PATH} -interp spline
-
-rv=$?
-
-echo `date`: task complete
-exit $rv
\ No newline at end of file