From a9dc2b4c633f8c432fd7bf66db9b562e6a113eb6 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 13 Jul 2023 10:42:49 +0100
Subject: [PATCH] TEST: Test for typical/standard MMORF run; needs
external/shared data
---
mmorf/feedsInputs | 1 +
mmorf/feedsRun | 93 +++++++++++++++++++++++++++++++++++++++++
mmorf/mov_to_ref_mm.ini | 60 ++++++++++++++++++++++++++
3 files changed, 154 insertions(+)
create mode 100755 mmorf/feedsInputs
create mode 100755 mmorf/feedsRun
create mode 100644 mmorf/mov_to_ref_mm.ini
diff --git a/mmorf/feedsInputs b/mmorf/feedsInputs
new file mode 100755
index 0000000..1bf9533
--- /dev/null
+++ b/mmorf/feedsInputs
@@ -0,0 +1 @@
+mmorf/
diff --git a/mmorf/feedsRun b/mmorf/feedsRun
new file mode 100755
index 0000000..89dbb0f
--- /dev/null
+++ b/mmorf/feedsRun
@@ -0,0 +1,93 @@
+#!/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}
+
+echo "----------"
+echo "MMORF Test"
+echo "----------"
+echo ""
+
+# Run MMORF
+echo ""
+echo "-------------"
+echo "Running mmorf"
+echo "-------------"
+echo ""
+mmorf --version --config ${MMORF_CONFIG}
+
+# 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 ""
diff --git a/mmorf/mov_to_ref_mm.ini b/mmorf/mov_to_ref_mm.ini
new file mode 100644
index 0000000..2bd0869
--- /dev/null
+++ b/mmorf/mov_to_ref_mm.ini
@@ -0,0 +1,60 @@
+; Values only set once
+warp_res_init = 32
+warp_scaling = 1 1 2 2
+img_warp_space = ##MMORF_INPUT_DIR##/ref/t1
+lambda_reg = 4.0e5 3.7e-1 3.1e-1 2.6e-1
+hires = 12
+optimiser_max_it_lowres = 5
+optimiser_max_it_hires = 5
+
+; T1 with no masking and no bias field
+img_ref_scalar = ##MMORF_INPUT_DIR##/ref/t1
+img_mov_scalar = ##MMORF_INPUT_DIR##/mov/t1
+aff_ref_scalar = ##MMORF_INPUT_DIR##/ref/identity.mat
+aff_mov_scalar = ##MMORF_INPUT_DIR##/mov/mov_to_ref.mat
+use_implicit_mask = 0
+use_mask_ref_scalar = 0 0 0 0
+use_mask_mov_scalar = 0 0 0 0
+mask_ref_scalar = NULL
+mask_mov_scalar = NULL
+fwhm_ref_scalar = 8.0 8.0 4.0 2.0
+fwhm_mov_scalar = 8.0 8.0 4.0 2.0
+lambda_scalar = 0.1 0.1 0.1 0.1
+estimate_bias = 0
+bias_res_init = 16
+lambda_bias_reg = 1e9 1e9 1e9 1e9
+
+; T1 with masking and bias field
+img_ref_scalar = ##MMORF_INPUT_DIR##/ref/t1
+img_mov_scalar = ##MMORF_INPUT_DIR##/mov/t1
+aff_ref_scalar = ##MMORF_INPUT_DIR##/ref/identity.mat
+aff_mov_scalar = ##MMORF_INPUT_DIR##/mov/mov_to_ref.mat
+use_implicit_mask = 0
+use_mask_ref_scalar = 1 1 1 1
+use_mask_mov_scalar = 1 1 1 1
+mask_ref_scalar = ##MMORF_INPUT_DIR##/ref/mask_t1
+mask_mov_scalar = ##MMORF_INPUT_DIR##/mov/mask_t1
+fwhm_ref_scalar = 8.0 8.0 4.0 2.0
+fwhm_mov_scalar = 8.0 8.0 4.0 2.0
+lambda_scalar = 1 1 1 1
+estimate_bias = 1
+bias_res_init = 16
+lambda_bias_reg = 1e9 1e9 1e9 1e9
+
+; First tensor pair
+img_ref_tensor = ##MMORF_INPUT_DIR##/ref/dti
+img_mov_tensor = ##MMORF_INPUT_DIR##/mov/dti
+aff_ref_tensor = ##MMORF_INPUT_DIR##/ref/identity.mat
+aff_mov_tensor = ##MMORF_INPUT_DIR##/mov/mov_to_ref.mat
+use_mask_ref_tensor = 1 1 1 1
+use_mask_mov_tensor = 1 1 1 1
+mask_ref_tensor = ##MMORF_INPUT_DIR##/ref/mask_dti
+mask_mov_tensor = ##MMORF_INPUT_DIR##/mov/mask_dti
+fwhm_ref_tensor = 8.0 8.0 4.0 2.0
+fwhm_mov_tensor = 8.0 8.0 4.0 2.0
+lambda_tensor = 1 1 1 1
+
+; Output warp
+warp_out = ##MMORF_OUTPUT_DIR##/out/mov_to_ref_warp
+jac_det_out = ##MMORF_OUTPUT_DIR##/out/mov_to_ref_jac
+bias_out = ##MMORF_OUTPUT_DIR##/out/mov_to_ref_bias
\ No newline at end of file
--
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