Quality Control

Including quality control (QC) steps within your module

When applicable, each module should include its own quality control (QC) steps compatible with the MultiQC report. This step should be run only if specified in the nextflow.config file, using the ext.run_qc scope. The QC can take different form depending on which processing steps are performed within your module. Common types are:

• Static image : .png, .jpeg, .tiff, … (e.g. overlay of labels/segmentation on T1w image),
• Dynamic image : .gif, .webp, … (e.g. dynamic change between pre and post processing),
• Tabular values : .txt, .csv, .tsv, … (e.g. summary statistics, quality metrics).

Typically, the images are created using the mid slice for all three axes and then combined into a mosaic using ImageMagick. Below is a code snippet giving general instructions or guidelines for this QC section:

    if $run_qc;
    then
        # Start by extracting the dimension of your image, then store it into a
        # single variable for each axis.
        extract_dim=\$(mrinfo ${prefix}__<image>.nii.gz -size)
        read sagittal_dim axial_dim coronal_dim <<< "\${extract_dim}"

        # Get the middle slice
        coronal_dim=\$((\$coronal_dim / 2))
        axial_dim=\$((\$axial_dim / 2))
        sagittal_dim=\$((\$sagittal_dim / 2))

        # Set visualization parameters to be applied to all images.
        viz_params="--display_slice_number --display_lr --size 256 256"

        # Sometimes, it might be useful to normalize the intensities to ensure
        # its consistency across images.
        scil_volume_math.py normalize_max ${prefix}__<image>.nii.gz \
          ${prefix}__<image>_norm.nii.gz

        # Do the actual screenshotting (adapt to your needs).
        scil_viz_volume_screenshot.py ${prefix}__<image>_norm.nii.gz \
          ${prefix}__<image>_coronal.png \${viz_params} --slices \${coronal_dim} \
          --axis coronal
        <...>

        # To create mosaics, use [ImageMagick](https://imagemagick.org/index.php).
        convert ${prefix}_<image>_axial*.png ${prefix}_<image>_coronal*.png \
          ${prefix}_<image>_saggital*.png +append ${prefix}_<image>_mqc.png

        # Clean up the intermediate pngs and norm image.
        rm ${prefix}_<image>_axial*.png ${prefix}_<image>_coronal*.png ${prefix}_<image>_saggital*.png
        rm *_norm.nii.gz
    fi

For simplicity, we will not add a QC step for the current denoising/nlmeans module. For more complete example, you can refer to the preproc/topup, preproc/eddy, or registration/anattodwi module.