Commit 04f3aef6 authored by Christoph Arthofer's avatar Christoph Arthofer
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parent 149ed012
#!/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}
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