TEST: Test for typical/standard MMORF run; needs external/shared data

mmorf/feedsInputs

+mmorf/

mmorf/feedsRun

+#!/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 ""

mmorf/mov_to_ref_mm.ini

+; 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
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