Upload cmore_mmorf.sh

OB_pipeline/cmore_mmorf.sh

+#!/bin/bash
+
+#$ -cwd -j y
+#$ -r y
+
+export SINGULARITY_BIND="/absolute/path/to/parent/directory/"
+
+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
+
+REF_DIR=$2
+IMG_REF_ID=$3
+IMG_T1_HEAD_REF_PATH="${REF_DIR}${IMG_REF_ID}_T1_head.nii.gz"
+IMG_T1_BRAIN_REF_PATH="${REF_DIR}${IMG_REF_ID}_T1_brain.nii.gz"
+IMG_T2_HEAD_REF_PATH="${REF_DIR}${IMG_REF_ID}_T2_head.nii.gz"
+
+ID_PATH=$1
+DATA_DIR=$5
+IMG_IN_ID=$(awk 'NR=='${SGE_TASK_ID} ${ID_PATH})
+IMG_T1_HEAD_IN_PATH="${DATA_DIR}${IMG_IN_ID}/T1/T1_unbiased.nii.gz"
+IMG_T1_BRAIN_IN_PATH="${DATA_DIR}${IMG_IN_ID}/T1/T1_unbiased_brain.nii.gz"
+IMG_T2_HEAD_IN_PATH="${DATA_DIR}${IMG_IN_ID}/T2_FLAIR/T2_FLAIR_unbiased.nii.gz"
+
+AFFINE_DIR=$4
+OMAT_T1_IN_PATH="${AFFINE_DIR}${IMG_IN_ID}_to_T1_unbiased_affine_template_MNI_T1_brain_T1reg.mat"
+OMAT_T2_IN_PATH="${AFFINE_DIR}${IMG_IN_ID}_to_T1_unbiased_affine_template_MNI_T1_brain_T2reg.mat"
+UNITY_REF_PATH="${FSLDIR}/etc/flirtsch/ident.mat"
+
+OUT_DIR=$6
+IMG_T1_HEAD_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_T1.nii.gz"
+IMG_T1_BRAIN_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_T1_brain.nii.gz"
+
+WARP_OUT="${OUT_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_warp.nii.gz"
+JAC_OUT="${OUT_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_jac.nii.gz"
+BIAS_OUT="${OUT_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_bias"
+
+PARAM_PATH="${OUT_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_params.ini"
+PARAM_IT_PATH=$7
+
+singularity run --nv mmorf.sif \
+--config ${PARAM_IT_PATH} \
+--img_warp_space ${IMG_T1_HEAD_REF_PATH} \
+--img_ref_scalar ${IMG_T1_HEAD_REF_PATH} \
+--img_mov_scalar ${IMG_T1_HEAD_IN_PATH} \
+--aff_ref_scalar ${UNITY_REF_PATH} \
+--aff_mov_scalar ${OMAT_T1_IN_PATH} \
+--mask_ref_scalar NULL \
+--mask_mov_scalar NULL \
+--img_ref_scalar ${IMG_T1_BRAIN_REF_PATH} \
+--img_mov_scalar ${IMG_T1_BRAIN_IN_PATH} \
+--aff_ref_scalar ${UNITY_REF_PATH} \
+--aff_mov_scalar ${OMAT_T1_IN_PATH} \
+--mask_ref_scalar NULL \
+--mask_mov_scalar NULL \
+--img_ref_scalar ${IMG_T2_HEAD_REF_PATH} \
+--img_mov_scalar ${IMG_T2_HEAD_IN_PATH} \
+--aff_ref_scalar ${UNITY_REF_PATH} \
+--aff_mov_scalar ${OMAT_T2_IN_PATH} \
+--mask_ref_scalar NULL \
+--mask_mov_scalar NULL \
+--warp_out ${WARP_OUT} \
+--jac_det_out ${JAC_OUT} \
+--bias_out ${BIAS_OUT}
+
+rv=$?
+
+echo `date`: task complete
+exit $rv
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