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add reference RGB #36

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Merged
arnaudbore merged 1 commit into from
Jan 28, 2026
Merged

add reference RGB #36

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5 changes: 5 additions & 0 deletions assets/multiqc_config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,11 @@ custom_data:
description: |
RGB map from RAW data versus RGB map after gradient correction. Corpus callosum should be in red.
### **Using the option use_preqc is highly experimental. Please be careful.**
<div style="background-color: #ffcccc; color: red; padding: 10px; border: 2px solid red;">
Be careful: If the colours match the reference image, it is important to ALSO look at the
eigenvectors of the tensors from the DTI model located in the folder (<code>dwi/sub-01_model-tensor_param-v1_dwimap.nii.gz</code>)
to ensure that the orientation is correct (see <a href="https://scilus.github.io/nf-mouse/guides/faq/" target="_blank">FAQ</a>).
</div>
plot_type: "image"

pre_qc_sampling_mqc:
Expand Down
Binary file modified assets/nf-mouse-light-logo.png
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Binary file added assets/reference_rgb_mqc.png
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7 changes: 5 additions & 2 deletions main.nf
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Expand Up @@ -49,10 +49,12 @@ workflow get_data {
mask_channel = Channel.fromPath("$input/**/*mask.nii.gz")
.map { mask_file -> def sid = mask_file.parent.name
[[id: sid], mask_file] }
template_channel = Channel.fromPath("$projectDir/assets/reference_rgb_mqc.png")

emit:
dwi = dwi_channel
mask = mask_channel
template_rgb = template_channel
}

workflow {
Expand All @@ -77,9 +79,10 @@ workflow {
bval: [meta, bval]
bvec: [meta, bvec]
}
ch_ref_rgb = data.template_rgb

if ( params.run_preqc ) {
PRE_QC(ch_dwi_bvalbvec.dwi.join(ch_dwi_bvalbvec.bvs_files))
PRE_QC(ch_dwi_bvalbvec.dwi.join(ch_dwi_bvalbvec.bvs_files).combine(ch_ref_rgb))
ch_multiqc_files = ch_multiqc_files.mix(PRE_QC.out.rgb_mqc)
ch_multiqc_files = ch_multiqc_files.mix(PRE_QC.out.sampling_mqc)
if (params.use_preqc){
Expand Down Expand Up @@ -222,5 +225,5 @@ workflow {
return tuple(meta, files)
}

MULTIQC(ch_multiqc_files, [], ch_multiqc_config.toList(), [], channel.fromPath("${projectDir}/assets/logo_bg.png").toList(), [], [])
MULTIQC(ch_multiqc_files, [], ch_multiqc_config.toList(), [], channel.fromPath("${projectDir}/assets/nf-mouse-light-logo.png").toList(), [], [])
}
6 changes: 3 additions & 3 deletions modules/local/mouse/preqc/main.nf
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Expand Up @@ -5,7 +5,7 @@ process PRE_QC {
container "scilus/scilus:2.2.0"

input:
tuple val(meta), path(dwi), path(bval), path(bvec)
tuple val(meta), path(dwi), path(bval), path(bvec), path(ref_rgb)

output:
tuple val(meta), path("*__stride_dwi.nii.gz") , emit: dwi
Expand Down Expand Up @@ -115,11 +115,11 @@ process PRE_QC {
${prefix}__sag_slice_\${mid_slice_sagittal}.png \
${prefix}_rgb_\${p}_mqc.png

convert -annotate +20+230 "RGB \${p}" -fill white -pointsize 30 ${prefix}_rgb_\${p}_mqc.png ${prefix}_rgb_\${p}_mqc.png
convert -annotate +20+40 "RGB \${p}" -fill white -pointsize 30 -undercolor black ${prefix}_rgb_\${p}_mqc.png ${prefix}_rgb_\${p}_mqc.png

rm -rf *_slice_*png
done
convert -append ${prefix}_rgb_pre_mqc.png ${prefix}_rgb_post_mqc.png ${prefix}__rgb_mqc.png
convert -append ${prefix}_rgb_pre_mqc.png ${prefix}_rgb_post_mqc.png $ref_rgb ${prefix}__rgb_mqc.png

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down