Initial implementation of antsRegistration_affine_SyN.sh

modules/nf-neuro/registration/cobralab_ants/environment.yml

@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: registration_ants

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

@@ -0,0 +1,188 @@
+
+process REGISTRATION_COBRALABANTS {
+    tag "$meta.id"
+    label 'process_medium'
+
+    container "scilus/scilus:2.2.1"
+
+    input:
+        tuple val(meta), path(fixed_image), path(moving_image), path(mask)
+
+    output:
+        tuple val(meta), path("*_warped.nii.gz")                           , emit: image_warped
+        tuple val(meta), path("*_forward1_affine.mat")                     , emit: forward_affine, optional: true
+        tuple val(meta), path("*_forward0_warp.nii.gz")                    , emit: forward_warp, optional: true
+        tuple val(meta), path("*_backward1_warp.nii.gz")                   , emit: backward_warp, optional: true
+        tuple val(meta), path("*_backward0_affine.mat")                    , emit: backward_affine, optional: true
+        tuple val(meta), path("*_forward*.{nii.gz,mat}", arity: '1..2')    , emit: forward_image_transform
+        tuple val(meta), path("*_backward*.{nii.gz,mat}", arity: '1..2')   , emit: backward_image_transform
+        tuple val(meta), path("*_backward*.{nii.gz,mat}", arity: '1..2')   , emit: forward_tractogram_transform
+        tuple val(meta), path("*_forward*.{nii.gz,mat}", arity: '1..2')    , emit: backward_tractogram_transform
+        tuple val(meta), path("*_registration_ants_mqc.gif")               , emit: mqc, optional: true
+        path "versions.yml"                                                , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix_qc = task.ext.suffix_qc ?: ""
+    def run_qc = task.ext.run_qc as Boolean || false
+
+    if ( mask ) args += " --fixed-mask $mask"
+    // if ( moving_mask ) args += " --moving-mask $moving_mask"
+    if ( task.ext.initial_transform ) args += " --initial-transform $task.ext.initial_transform"
+    if ( task.ext.float ) args += " --float"
+    if ( task.ext.histogram_matching ) args += " --histogram-matching"
+    if ( task.ext.rough ) args += " --rough"
+    if ( task.ext.fast ) args += " --fast"
+    if ( task.ext.mask_extract ) args += " --mask-extract"
+    if ( task.ext.keep_mask_after_extract ) args += " --keep-mask-after-extract"
+    if ( task.ext.resampled_linear_output ) args += " --resampled-linear-output $task.ext.resampled_linear_output"
+    if ( task.ext.linear_type ) args += " --linear-type $task.ext.linear_type"
+    if ( task.ext.close ) args += " --close"
+    if ( task.ext.convergence != '1e-6' ) args += " --convergence $task.ext.convergence"
+    if ( task.ext.skip_linear ) args += " --skip-linear"
+    if ( task.ext.linear_metric != 'Mattes' ) args += " --linear-metric $task.ext.linear_metric"
+    if ( task.ext.linear_shrink_factors ) args += " --linear-shrink-factors $task.ext.linear_shrink_factors"
+    if ( task.ext.linear_smoothing_sigmas ) args += " --linear-smoothing-sigmas $task.ext.linear_smoothing_sigmas"
+    if ( task.ext.linear_convergence ) args += " --linear-convergence $task.ext.linear_convergence"
+    if ( task.ext.final_iterations_linear != '50' ) args += " --final-iterations-linear $task.ext.final_iterations_linear"
+    if ( task.ext.kmeans_transformed_linear ) args += " --kmeans-transformed-linear"
+    if ( task.ext.skip_nonlinear ) args += " --skip-nonlinear"
+    if ( task.ext.syn_control != '0.4,4,0' ) args += " --syn-control $task.ext.syn_control"
+    if ( task.ext.syn_metric != 'CC[4]' ) args += " --syn-metric $task.ext.syn_metric"
+    if ( task.ext.syn_shrink_factors ) args += " --syn-shrink-factors $task.ext.syn_shrink_factors"
+    if ( task.ext.syn_smoothing_sigmas ) args += " --syn-smoothing-sigmas $task.ext.syn_smoothing_sigmas"
+    if ( task.ext.syn_convergence ) args += " --syn-convergence $task.ext.syn_convergence"
+    if ( task.ext.final_iterations_nonlinear != '20' ) args += " --final-iterations-nonlinear $task.ext.final_iterations_nonlinear"
+    if ( task.ext.winsorize_image_intensities ) args += " --winsorize-image-intensities $task.ext.winsorize_image_intensities"
+    if ( task.ext.clobber ) args += " --clobber"
+    if ( task.ext.verbose == false ) args += " --no-verbose"
+    if ( task.ext.debug ) args += " --debug"
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=$task.cpus
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    moving_id=\$(basename $moving_image .nii.gz)
+    moving_id=\${moving_id#${meta.id}_*}
+
+    antsRegistration_affine_SyN.sh $args --resampled-output ${prefix}_\${moving_id}_warped.nii.gz $moving_image $fixed_image output
+
+    if [ ${task.ext.skip_linear} == false ]; then
+        mv output0GenericAffine.mat ${prefix}_forward1_affine.mat
+    fi
+
+    if [ ${task.ext.skip_nonlinear} == false ]; then
+        mv output1InverseWarp.nii.gz ${prefix}_backward1_warp.nii.gz
+        mv output1Warp.nii.gz ${prefix}_forward0_warp.nii.gz
+    fi
+
+    antsApplyTransforms -d 3 -t [${prefix}_forward1_affine.mat,1] \
+        -o Linear[${prefix}_backward0_affine.mat]
+
+    ### ** QC ** ###
+    if $run_qc; then
+        mv $fixed_image fixed_image.nii.gz
+        extract_dim=\$(mrinfo fixed_image.nii.gz -size)
+        read sagittal_dim coronal_dim axial_dim <<< "\${extract_dim}"
+
+        # Get the middle slice
+        coronal_dim=\$((\$coronal_dim / 2))
+        axial_dim=\$((\$axial_dim / 2))
+        sagittal_dim=\$((\$sagittal_dim / 2))
+
+        # Get fixed ID, moving ID already computed
+        fixed_id=\$(basename $fixed_image .nii.gz)
+        fixed_id=\${fixed_id#${meta.id}_*}
+
+        # Set viz params.
+        viz_params="--display_slice_number --display_lr --size 256 256"
+        # Iterate over images.
+        for image in fixed_image warped; do
+            mrconvert *\${image}.nii.gz *\${image}_viz.nii.gz -stride -1,2,3
+            scil_viz_volume_screenshot *\${image}_viz.nii.gz \${image}_coronal.png \
+                --slices \$coronal_dim --axis coronal \$viz_params
+            scil_viz_volume_screenshot *\${image}_viz.nii.gz \${image}_sagittal.png \
+                --slices \$sagittal_dim --axis sagittal \$viz_params
+            scil_viz_volume_screenshot *\${image}_viz.nii.gz \${image}_axial.png \
+                --slices \$axial_dim --axis axial \$viz_params
+
+            if [ \$image != fixed_image ]; then
+                title="Warped \${moving_id^^}"
+            else
+                title="Reference \${fixed_id^^}"
+            fi
+
+            convert +append \${image}_coronal*.png \${image}_axial*.png \
+                \${image}_sagittal*.png \${image}_mosaic.png
+            convert -annotate +20+230 "\${title}" -fill white -pointsize 30 \
+                \${image}_mosaic.png \${image}_mosaic.png
+
+            # Clean up.
+            rm \${image}_coronal*.png \${image}_sagittal*.png \${image}_axial*.png
+        done
+
+        # Create GIF.
+        convert -delay 10 -loop 0 -morph 10 \
+            warped_mosaic.png fixed_image_mosaic.png warped_mosaic.png \
+            ${prefix}_${suffix_qc}_registration_ants_mqc.gif
+
+        # Clean up.
+        rm *_mosaic.png
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*: v?([0-9.a-zA-Z-]+).*/\\1/')
+        imagemagick: \$(convert -version | grep "Version:" | sed -E 's/.*ImageMagick ([0-9.-]+).*/\\1/')
+        mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix_qc = task.ext.suffix_qc ?: ""
+    def run_qc = task.ext.run_qc as Boolean || false
+
+    """
+    set +e
+    function handle_code () {
+        local code=\$?
+        ignore=( 1 )
+        [[ " \${ignore[@]} " =~ " \$code " ]] || exit \$code
+    }
+
+    # Local trap to ignore awaited non-zero exit codes
+    {
+        trap 'handle_code' ERR
+        antsRegistrationSyNQuick.sh -h
+    }
+
+    antsApplyTransforms -h
+    convert -help .
+    scil_viz_volume_screenshot -h
+
+    touch ${prefix}_t1_warped.nii.gz
+    touch ${prefix}_forward1_affine.mat
+    touch ${prefix}_forward0_warp.nii.gz
+    touch ${prefix}_backward1_warp.nii.gz
+    touch ${prefix}_backward0_affine.mat
+
+    if $run_qc; then
+        touch ${prefix}_${suffix_qc}_registration_ants_mqc.gif
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*: v?([0-9.a-zA-Z-]+).*/\\1/')
+        imagemagick: \$(convert -version | grep "Version:" | sed -E 's/.*ImageMagick ([0-9.-]+).*/\\1/')
+        mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+}