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OB_pipeline/cmore_FLIRT_registration.sh

+#!/bin/bash
+
+# Author: Christoph Arthofer
+# Copyright: FMRIB 2021
+
+#$ -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
+TEMP_DIR=$3
+OUT_DIR=$4
+
+IMG_IN_ID=$(awk 'NR=='${SGE_TASK_ID} ${ID_PATH})
+
+IMG_IN_PATH="${DATA_DIR}${IMG_IN_ID}/T1/T1_unbiased_brain.nii.gz"
+IMG_REF_PATH="${TEMP_DIR}T1_template_brain.nii.gz"
+T1_OMAT_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_to_template_T1reg.mat"
+
+echo "flirt -in ${IMG_IN_PATH} -ref ${IMG_REF_PATH} -omat ${T1_OMAT_OUT_PATH} -dof 12"
+flirt -in ${IMG_IN_PATH} -ref ${IMG_REF_PATH} -omat ${T1_OMAT_OUT_PATH} -dof 12
+
+
+
+IMG_IN_PATH="${DATA_DIR}${IMG_IN_ID}/T2_FLAIR/T2_FLAIR_unbiased_brain.nii.gz"
+IMG_REF_PATH="${DATA_DIR}${IMG_IN_ID}/T1/T1_unbiased_brain.nii.gz"
+T2_to_T1_OMAT_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_T2_to_T1.mat"
+
+echo "flirt -in ${IMG_IN_PATH} -ref ${IMG_REF_PATH} -omat ${T2_to_T1_OMAT_OUT_PATH} -dof 6"
+flirt -in ${IMG_IN_PATH} -ref ${IMG_REF_PATH} -omat ${T2_to_T1_OMAT_OUT_PATH} -dof 6
+
+
+
+T2_OMAT_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_to_template_T2reg.mat"
+echo "convert_xfm -omat ${T2_OMAT_OUT_PATH} -concat ${T1_OMAT_OUT_PATH} ${T2_to_T1_OMAT_OUT_PATH}"
+
+convert_xfm -omat ${T2_OMAT_OUT_PATH} -concat ${T1_OMAT_OUT_PATH} ${T2_to_T1_OMAT_OUT_PATH}
+
+rv=$?
+
+echo `date`: task complete
+exit $rv
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