Upload New File

OB_pipeline/cmore_run_reg2template.sh

+#!/bin/bash
+
+# Author: Christoph Arthofer
+# Copyright: FMRIB 2021
+
+
+TAG='cmore'
+BASE_DIR="cmore/data/output/"
+DATA_DIR="cmore/data/orig/"
+ID_PATH="cmore/data/IDs.csv"
+TEMP_DIR="cmore/data/template/"
+PARAM_IT_PATH="cmore/data/mmorf_params_it18.ini"
+
+N_IMGS=$(cat ${ID_PATH} | wc -l)
+i_outp=0
+
+# Create output directory for affine registrations
+AFFINE_DIR="${BASE_DIR}affine_it1/"
+mkdir -p ${AFFINE_DIR}
+
+# Register all individual images to one reference image
+i_outp=$((i_outp+1))
+printf -v i "%04d" $i_outp
+qsub -o ${BASE_DIR}${i}_output_affine_FLIRT_testing.log \
+  -N ${TAG}_registrations_affine_testing_it1 \
+  -q short.qc \
+  -t 1-${N_IMGS}:1 \
+  cmore_FLIRT_registration.sh ${ID_PATH} ${DATA_DIR} ${TEMP_DIR} ${AFFINE_DIR}
+
+# ----------------------------------------------------------------------------------------------------------------------
+# Nonlinear registrations
+NLN_DIR="${BASE_DIR}nln_testing_it1/"
+mkdir -p ${NLN_DIR}
+
+i_outp=$((i_outp+1))
+printf -v i "%04d" $i_outp
+REF_DIR=${NLN_REF_DIR}
+qsub -hold_jid ${TAG}_registrations_affine_testing_it1 \
+  -o ${BASE_DIR}${i}_output_nln_registrations_it1.log \
+  -N ${TAG}_registrations_mmorf \
+  -q gpu8.q \
+  -l gpu=1 \
+  -l gputype=p100 \
+  -t 1-${N_IMGS}:1 \
+  cmore_mmorf.sh ${ID_PATH} ${TEMP_DIR} ${DATA_DIR} ${AFFINE_DIR} ${NLN_DIR} ${PARAM_IT_PATH}
+
+i_outp=$((i_outp+1))
+printf -v i "%04d" $i_outp
+qsub -hold_jid ${TAG}_registrations_mmorf \
+  -o ${BASE_DIR}${i}_output_cmore_inverseWarps.log \
+  -N ${TAG}_invertWarps \
+  -q short.qc \
+  -t 1-${N_IMGS}:1 \
+  cmore_invertWarps.sh ${ID_PATH} ${DATA_DIR} ${NLN_DIR} ${TEMP_DIR}