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#!/usr/bin/env bash
set -e
thisdir=$(cd $(dirname $0) && pwd)
outdir=$1
indir=$2/mmorf
benchmarkdir=$3
mkdir -p ${outdir}/out
MMORF_CONFIG=${outdir}/mmorf_config.ini
cat mov_to_ref_mm.ini | \
sed "s%##MMORF_INPUT_DIR##%${indir}%g" | \
sed "s%##MMORF_OUTPUT_DIR##%${outdir}%g" > \
${MMORF_CONFIG}
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committed
echo "-----------"
echo "MMORF Test: $(which mmorf)"
echo "-----------"
echo ""
# Run MMORF
echo ""
echo "-------------"
echo "Running mmorf"
echo "-------------"
echo ""
# Use fsl_sub in case we are running on the
# cluster. This will just run normally if running
# locally (but fsl_sub will still return a job id
# that can be used in the subsequent hold call).
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committed
job_id=$(fsl_sub --coprocessor=cuda --logdir=${outdir} mmorf --version --config ${MMORF_CONFIG})
touch ${outdir}/wait
fsl_sub --jobhold ${job_id} rm ${outdir}/wait
while [ -e ${outdir}/wait ]; do
sleep 1m
done
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# Combine warps
echo ""
echo "-------------------"
echo "Running convertwarp"
echo "-------------------"
echo ""
convertwarp -m ${indir}/mov/mov_to_ref.mat -w ${outdir}/out/mov_to_ref_warp -r ${indir}/ref/t1 -o ${outdir}/out/mov_to_ref_warp_combined --rel --relout
# Resample T1
echo ""
echo "-----------------"
echo "Running applywarp"
echo "-----------------"
echo ""
applywarp -i ${indir}/mov/t1 -r ${indir}/ref/t1 -w ${outdir}/out/mov_to_ref_warp_combined -o ${outdir}/out/mov_to_ref_t1_nln
# Resample DTI
echo ""
echo "--------------"
echo "Running vecreg"
echo "--------------"
echo ""
vecreg -i ${indir}/mov/dti -o ${outdir}/out/mov_to_ref_dti_nln -r ${indir}/ref/t1 -w ${outdir}/out/mov_to_ref_warp_combined -m ${indir}/mov/mask_dti --refmask=${indir}/ref/mask_dti
# Calculate squared differences to expected outputs
echo ""
echo "----------------"
echo "Running fslmaths"
echo "----------------"
echo ""
fslmaths ${outdir}/out/mov_to_ref_warp -inm 1000 ${outdir}/out/mov_to_ref_warp
fslmaths ${outdir}/out/mov_to_ref_warp_combined -inm 1000 ${outdir}/out/mov_to_ref_warp_combined
fslmaths ${outdir}/out/mov_to_ref_jac -inm 1000 ${outdir}/out/mov_to_ref_jac
fslmaths ${outdir}/out/mov_to_ref_bias_1 -inm 1000 ${outdir}/out/mov_to_ref_bias_1
fslmaths ${outdir}/out/mov_to_ref_t1_nln -inm 1000 ${outdir}/out/mov_to_ref_t1_nln
fslmaths ${outdir}/out/mov_to_ref_dti_nln -inm 1000 ${outdir}/out/mov_to_ref_dti_nln
fslmaths ${outdir}/out/mov_to_ref_warp -sub ${benchmarkdir}/out/mov_to_ref_warp -sqr -Tmean ${outdir}/out/mov_to_ref_warp_sd
fslmaths ${outdir}/out/mov_to_ref_warp_combined -sub ${benchmarkdir}/out/mov_to_ref_warp_combined -sqr -Tmean ${outdir}/out/mov_to_ref_warp_combined_sd
fslmaths ${outdir}/out/mov_to_ref_jac -sub ${benchmarkdir}/out/mov_to_ref_jac -sqr ${outdir}/out/mov_to_ref_jac_sd
fslmaths ${outdir}/out/mov_to_ref_bias_1 -sub ${benchmarkdir}/out/mov_to_ref_bias_1 -sqr ${outdir}/out/mov_to_ref_bias_1_sd
fslmaths ${outdir}/out/mov_to_ref_t1_nln -sub ${benchmarkdir}/out/mov_to_ref_t1_nln -sqr ${outdir}/out/mov_to_ref_t1_nln_sd
fslmaths ${outdir}/out/mov_to_ref_dti_nln -sub ${benchmarkdir}/out/mov_to_ref_dti_nln -sqr -Tmean ${outdir}/out/mov_to_ref_dti_nln_sd
# Calculate MSE for each output to expected output
echo ""
echo "----------------"
echo "Running fslstats"
echo "----------------"
echo ""
echo "Warp Field MSE = $(fslstats ${outdir}/out/mov_to_ref_warp_sd -k ${indir}/ref/mask_dti -m)"
echo "Jac Det MSE = $(fslstats ${outdir}/out/mov_to_ref_jac_sd -k ${indir}/ref/mask_dti -m)"
echo "Bias Field MSE = $(fslstats ${outdir}/out/mov_to_ref_bias_1_sd -k ${indir}/ref/mask_dti -m)"
echo "Combined Warp MSE = $(fslstats ${outdir}/out/mov_to_ref_warp_combined_sd -k ${indir}/ref/mask_dti -m)"
echo "T1 Nonlin MSE = $(fslstats ${outdir}/out/mov_to_ref_t1_nln_sd -k ${indir}/ref/mask_dti -m)"
echo "DTI Nonlin MSE = $(fslstats ${outdir}/out/mov_to_ref_dti_nln_sd -k ${indir}/ref/mask_dti -m)"
echo ""
echo "-------------"
echo "TEST COMPLETE"
echo "-------------"
echo ""