Upload cmore_applyxfm2T2.sh

OB_pipeline/cmore_applyxfm2T2.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}
+IN_DIR=${2}
+OUT_DIR=${IN_DIR}
+DATA_DIR=${3}
+IMG_REF_ID=${4}
+IMG_REF_PATH=${5}
+
+IMG_IN_ID=$(awk 'NR=='${SGE_TASK_ID} ${ID_PATH})
+
+T2_2_T1_OMAT_PATH="${IN_DIR}${IMG_IN_ID}_T2_to_T1.mat"
+T1_2_REF_PATH="${IN_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_T1reg.mat"
+T2_OMAT_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_T2reg.mat"
+
+convert_xfm -omat ${T2_OMAT_OUT_PATH} -concat ${T1_2_REF_PATH} ${T2_2_T1_OMAT_PATH}
+
+IMG_IN_PATH="${DATA_DIR}${IMG_IN_ID}/T2_FLAIR/T2_FLAIR_unbiased.nii.gz"
+IMG_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_T2reg.nii.gz"
+flirt -in ${IMG_IN_PATH} -ref ${IMG_REF_PATH} -out ${IMG_OUT_PATH} -applyxfm -init ${T2_OMAT_OUT_PATH} -interp spline
+
+rv=$?
+
+echo `date`: task complete
+exit $rv
\ No newline at end of file