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[BF] process bundle endpoints metrics #39

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[BF] process bundle endpoints metrics #39

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be31e02
fix process
arnaudbore Oct 29, 2025
918f62d
fix endpoint metrics with more than 10 dpp
arnaudbore Nov 5, 2025
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22 changes: 19 additions & 3 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -329,7 +329,6 @@ process Bundle_Label_And_Distance_Maps {
bname=\$(basename \$bundle .trk)
fi
bname=\${bname/_ic/}

centroid=${sid}__\${bname}_centroid_${params.nb_points}.trk
if [[ -f \${centroid} ]]; then
scil_bundle_label_map.py \$bundle \${centroid} tmp_out -f
Expand Down Expand Up @@ -636,10 +635,27 @@ process Bundle_Endpoints_Metrics {
b_metrics+=" afd_metric.nii.gz"
fi

scil_tractogram_project_streamlines_to_map.py \$bundle \${bname} --in_metrics \${b_metrics} --from_wm
IFS=' ' read -r -a all_items <<< "\${b_metrics}"

block_size=10
i=0
while [ \$i -lt \${#all_items[@]} ]; do
subset=("\${all_items[@]:\$i:\$block_size}")
scil_tractogram_project_map_to_streamlines.py \${bundle} \${bundle/.trk/_with_dpp.trk} \
--in_maps \${subset[@]} \
--out_dpp_name \${subset[@]//.nii.gz/} -f

scil_tractogram_project_streamlines_to_map.py \${bundle/.trk/_with_dpp.trk} \${bname}/ \
--use_dpp \${subset[@]//.nii.gz/} \
--mean_streamline \
--to_endpoints

((i += block_size))
done

cd \${bname}
for i in *.nii.gz;
do mv "\$i" "${sid}__\$i";
do mv "\$i" "${sid}__\${i/.nii.gz/_endpoints_metric.nii.gz}";
done

for i in *;
Expand Down