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Initial implementation of antsRegistration_affine_SyN.sh
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‎modules/nf-neuro/registration/cobralab_ants/environment.yml‎

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channels: []
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dependencies: []
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name: registration_ants

‎modules/nf-neuro/registration/cobralab_ants/main.nf‎

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process REGISTRATION_COBRALABANTS {
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tag "$meta.id"
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label 'process_medium'
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container "scilus/scilus:2.2.1"
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input:
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tuple val(meta), path(fixed_image), path(moving_image), path(mask), path(moving_mask, optional: true)
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output:
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tuple val(meta), path("*_warped.nii.gz") , emit: image_warped
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tuple val(meta), path("*_forward1_affine.mat") , emit: forward_affine, optional: true
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tuple val(meta), path("*_forward0_warp.nii.gz") , emit: forward_warp, optional: true
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tuple val(meta), path("*_backward1_warp.nii.gz") , emit: backward_warp, optional: true
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tuple val(meta), path("*_backward0_affine.mat") , emit: backward_affine, optional: true
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tuple val(meta), path("*_forward*.{nii.gz,mat}", arity: '1..2') , emit: forward_image_transform
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tuple val(meta), path("*_backward*.{nii.gz,mat}", arity: '1..2') , emit: backward_image_transform
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tuple val(meta), path("*_backward*.{nii.gz,mat}", arity: '1..2') , emit: forward_tractogram_transform
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tuple val(meta), path("*_forward*.{nii.gz,mat}", arity: '1..2') , emit: backward_tractogram_transform
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tuple val(meta), path("*_registration_ants_mqc.gif") , emit: mqc, optional: true
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def suffix_qc = task.ext.suffix_qc ?: ""
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def run_qc = task.ext.run_qc as Boolean || false
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if ( mask ) args += " --fixed-mask $mask"
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if ( moving_mask ) args += " --moving-mask $moving_mask"
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if ( task.ext.initial_transform ) args += " --initial-transform $task.ext.initial_transform"
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if ( task.ext.float ) args += " --float"
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if ( task.ext.histogram_matching ) args += " --histogram-matching"
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if ( task.ext.rough ) args += " --rough"
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if ( task.ext.fast ) args += " --fast"
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if ( task.ext.mask_extract ) args += " --mask-extract"
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if ( task.ext.keep_mask_after_extract ) args += " --keep-mask-after-extract"
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if ( task.ext.resampled_linear_output ) args += " --resampled-linear-output $task.ext.resampled_linear_output"
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if ( task.ext.linear_type ) args += " --linear-type $task.ext.linear_type"
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if ( task.ext.close ) args += " --close"
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if ( task.ext.convergence != '1e-6' ) args += " --convergence $task.ext.convergence"
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if ( task.ext.skip_linear ) args += " --skip-linear"
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if ( task.ext.linear_metric != 'Mattes' ) args += " --linear-metric $task.ext.linear_metric"
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if ( task.ext.linear_shrink_factors ) args += " --linear-shrink-factors $task.ext.linear_shrink_factors"
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if ( task.ext.linear_smoothing_sigmas ) args += " --linear-smoothing-sigmas $task.ext.linear_smoothing_sigmas"
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if ( task.ext.linear_convergence ) args += " --linear-convergence $task.ext.linear_convergence"
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if ( task.ext.final_iterations_linear != '50' ) args += " --final-iterations-linear $task.ext.final_iterations_linear"
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if ( task.ext.kmeans_transformed_linear ) args += " --kmeans-transformed-linear"
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if ( task.ext.skip_nonlinear ) args += " --skip-nonlinear"
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if ( task.ext.syn_control != '0.4,4,0' ) args += " --syn-control $task.ext.syn_control"
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if ( task.ext.syn_metric != 'CC[4]' ) args += " --syn-metric $task.ext.syn_metric"
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if ( task.ext.syn_shrink_factors ) args += " --syn-shrink-factors $task.ext.syn_shrink_factors"
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if ( task.ext.syn_smoothing_sigmas ) args += " --syn-smoothing-sigmas $task.ext.syn_smoothing_sigmas"
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if ( task.ext.syn_convergence ) args += " --syn-convergence $task.ext.syn_convergence"
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if ( task.ext.final_iterations_nonlinear != '20' ) args += " --final-iterations-nonlinear $task.ext.final_iterations_nonlinear"
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if ( task.ext.winsorize_image_intensities ) args += " --winsorize-image-intensities $task.ext.winsorize_image_intensities"
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if ( task.ext.clobber ) args += " --clobber"
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if ( task.ext.verbose == false ) args += " --no-verbose"
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if ( task.ext.debug ) args += " --debug"
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"""
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export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=$task.cpus
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export OMP_NUM_THREADS=1
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export OPENBLAS_NUM_THREADS=1
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moving_id=\$(basename $moving_image .nii.gz)
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moving_id=\${moving_id#${meta.id}_*}
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antsRegistration_affine_SyN.sh $args --resampled-output ${prefix}_\${moving_id}_warped.nii.gz $moving_image $fixed_image output
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if [ ${task.ext.skip_linear} == false ]; then
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mv output0GenericAffine.mat ${prefix}_forward1_affine.mat
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fi
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if [ ${task.ext.skip_nonlinear} == false ]; then
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mv output1InverseWarp.nii.gz ${prefix}_backward1_warp.nii.gz
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mv output1Warp.nii.gz ${prefix}_forward0_warp.nii.gz
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fi
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antsApplyTransforms -d 3 -t [${prefix}_forward1_affine.mat,1] \
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-o Linear[${prefix}_backward0_affine.mat]
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### ** QC ** ###
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if $run_qc; then
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mv $fixed_image fixed_image.nii.gz
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extract_dim=\$(mrinfo fixed_image.nii.gz -size)
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read sagittal_dim coronal_dim axial_dim <<< "\${extract_dim}"
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# Get the middle slice
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coronal_dim=\$((\$coronal_dim / 2))
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axial_dim=\$((\$axial_dim / 2))
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sagittal_dim=\$((\$sagittal_dim / 2))
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# Get fixed ID, moving ID already computed
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fixed_id=\$(basename $fixed_image .nii.gz)
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fixed_id=\${fixed_id#${meta.id}_*}
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# Set viz params.
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viz_params="--display_slice_number --display_lr --size 256 256"
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# Iterate over images.
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for image in fixed_image warped; do
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mrconvert *\${image}.nii.gz *\${image}_viz.nii.gz -stride -1,2,3
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scil_viz_volume_screenshot *\${image}_viz.nii.gz \${image}_coronal.png \
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--slices \$coronal_dim --axis coronal \$viz_params
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scil_viz_volume_screenshot *\${image}_viz.nii.gz \${image}_sagittal.png \
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--slices \$sagittal_dim --axis sagittal \$viz_params
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scil_viz_volume_screenshot *\${image}_viz.nii.gz \${image}_axial.png \
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--slices \$axial_dim --axis axial \$viz_params
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if [ \$image != fixed_image ]; then
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title="Warped \${moving_id^^}"
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else
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title="Reference \${fixed_id^^}"
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fi
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convert +append \${image}_coronal*.png \${image}_axial*.png \
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\${image}_sagittal*.png \${image}_mosaic.png
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convert -annotate +20+230 "\${title}" -fill white -pointsize 30 \
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\${image}_mosaic.png \${image}_mosaic.png
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# Clean up.
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rm \${image}_coronal*.png \${image}_sagittal*.png \${image}_axial*.png
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done
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# Create GIF.
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convert -delay 10 -loop 0 -morph 10 \
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warped_mosaic.png fixed_image_mosaic.png warped_mosaic.png \
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${prefix}_${suffix_qc}_registration_ants_mqc.gif
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# Clean up.
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rm *_mosaic.png
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*: v?([0-9.a-zA-Z-]+).*/\\1/')
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imagemagick: \$(convert -version | grep "Version:" | sed -E 's/.*ImageMagick ([0-9.-]+).*/\\1/')
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mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
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scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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def suffix_qc = task.ext.suffix_qc ?: ""
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def run_qc = task.ext.run_qc as Boolean || false
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"""
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set +e
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function handle_code () {
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local code=\$?
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ignore=( 1 )
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[[ " \${ignore[@]} " =~ " \$code " ]] || exit \$code
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}
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# Local trap to ignore awaited non-zero exit codes
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{
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trap 'handle_code' ERR
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antsRegistrationSyNQuick.sh -h
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}
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antsApplyTransforms -h
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convert -help .
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scil_viz_volume_screenshot -h
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touch ${prefix}_t1_warped.nii.gz
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touch ${prefix}_forward1_affine.mat
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touch ${prefix}_forward0_warp.nii.gz
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touch ${prefix}_backward1_warp.nii.gz
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touch ${prefix}_backward0_affine.mat
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if $run_qc; then
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touch ${prefix}_${suffix_qc}_registration_ants_mqc.gif
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*: v?([0-9.a-zA-Z-]+).*/\\1/')
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imagemagick: \$(convert -version | grep "Version:" | sed -E 's/.*ImageMagick ([0-9.-]+).*/\\1/')
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mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
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scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
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END_VERSIONS
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"""
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}

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