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harmonize_json #18

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merged 5 commits into from
Jun 29, 2023
Merged

harmonize_json #18

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cc45b8f
Fix missing data
frheault May 2, 2023
e06ed92
Fix afd and labels/distances duplicated
frheault May 29, 2023
a62a413
Extra space
frheault May 29, 2023
16837d7
No fodf bug fix, new labels map support
frheault Jun 21, 2023
1f33ce6
project
frheault Jun 22, 2023
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3 changes: 0 additions & 3 deletions USAGE
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Original file line number Diff line number Diff line change
Expand Up @@ -68,9 +68,6 @@ OPTIONAL ARGUMENTS (current value)
--use_provided_centroids Use the provided pre-computed centroids rather than using automatic computation ($use_provided_centroids)
--bundle_suffix_to_remove Use to remove the suffix from RBx-Flow ($bundle_suffix_to_remove)

--min_streamline_count Minimum streamline count threshold from trimming of 'edges' in the voxel labels map ($min_streamline_count)
--min_voxel_count Minimum voxel count threshold from trimming of 'edges' in the voxel labels map ($min_voxel_count)

--mean_std_density_weighting Weight the mean/std by the local tract density ($mean_std_density_weighting)
--mean_std_per_point_density_weighting Weight the mean/std per point by the local tract density ($mean_std_per_point_density_weighting)
--endpoints_metric_stats_normalize_weights Normalize the weights to the [0, 1] range ($endpoints_metric_stats_normalize_weights)
Expand Down
70 changes: 44 additions & 26 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -257,9 +257,7 @@ process Bundle_Label_And_Distance_Maps {

centroid=${sid}__\${bname}_centroid_${params.nb_points}.trk
if [[ -f \${centroid} ]]; then
scil_compute_bundle_voxel_label_map.py \$bundle \${centroid} tmp_out\
--min_streamline_count ${params.min_streamline_count} \
--min_voxel_count ${params.min_voxel_count} -f
scil_compute_bundle_voxel_label_map.py \$bundle \${centroid} tmp_out -f

mv tmp_out/labels_map.nii.gz ${sid}__\${bname}_labels.nii.gz
mv tmp_out/distance_map.nii.gz ${sid}__\${bname}_distances.nii.gz
Expand Down Expand Up @@ -445,7 +443,7 @@ process Bundle_Endpoints_Map {
metrics_for_endpoints_roi_stats
.mix(fixel_afd_for_endpoints_roi_stats)
.groupTuple(by: 0)
.map{it -> [it[0], it[1..-1].flatten()]}
.map{it -> [it[0], it[1..-1].flatten()]}
.set{metrics_afd_for_endpoints_roi_stats}

metrics_afd_for_endpoints_roi_stats
Expand Down Expand Up @@ -478,10 +476,13 @@ process Bundle_Metrics_Stats_In_Endpoints {
bname=\${bname/_endpoints_map_head/}
mv \$map \${bname}_head.nii.gz
mv \${map/_head/_tail} \${bname}_tail.nii.gz
if [ -f "\${bname}_afd_metric.nii.gz" ]; then
b_metrics="!(*afd*|*head*|*tail*).nii.gz \${bname}_afd_metric.nii.gz"
else
b_metrics="$metrics"

b_metrics=($metrics)
if [[ -f \${bname}_afd_metric.nii.gz ]];
then
mv \${bname}_afd_metric.nii.gz afd_metric.nii.gz
b_metrics="\${b_metrics[@]//*afd_metric*}"
b_metrics+=" afd_metric.nii.gz"
fi

scil_compute_metrics_stats_in_ROI.py \${bname}_head.nii.gz $normalize_weights\
Expand All @@ -498,7 +499,7 @@ process Bundle_Metrics_Stats_In_Endpoints {
metrics_for_endpoints_metrics
.mix(fixel_afd_for_endpoints_metrics)
.groupTuple(by: 0)
.map{it -> [it[0], it[1..-1].flatten()]}
.map{it -> [it[0], it[1..-1].flatten()]}
.set{metrics_afd_for_endpoints_metrics}

bundles_for_endpoints_metrics
Expand Down Expand Up @@ -529,17 +530,19 @@ process Bundle_Endpoints_Metrics {
fi
bname=\${bname/_uniformized/}
mkdir \${bname}
if [ -f "\${bname}_afd_metric.nii.gz" ]; then
b_metrics="!(*afd*).nii.gz \${bname}_afd_metric.nii.gz"
else
b_metrics="$metrics"

b_metrics=($metrics)
if [[ -f \${bname}_afd_metric.nii.gz ]];
then
mv \${bname}_afd_metric.nii.gz afd_metric.nii.gz
b_metrics="\${b_metrics[@]//*afd_metric*}"
b_metrics+=" afd_metric.nii.gz"
fi

scil_compute_endpoints_metric.py \$bundle \${b_metrics} \${bname}
scil_project_streamlines_to_map.py \$bundle \${bname} --in_metrics \${b_metrics} --from_wm
cd \${bname}
for i in *.nii.gz;
do
mv "\$i" "${sid}__\$i";
do mv "\$i" "${sid}__\$i";
done
rename s/${sid}__${sid}__/${sid}__/ *

Expand All @@ -549,7 +552,7 @@ process Bundle_Endpoints_Metrics {
metrics_for_mean_std
.mix(fixel_afd_for_mean_std)
.groupTuple(by: 0)
.map{it -> [it[0], it[1..-1].flatten()]}
.map{it -> [it[0], it[1..-1].flatten()]}
.set{metrics_afd_for_mean_std}

metrics_afd_for_mean_std
Expand Down Expand Up @@ -579,11 +582,14 @@ process Bundle_Mean_Std {
bname=\${bname/_uniformized/}
mv \$bundle \$bname.trk

if [ -f "\${bname}_afd_metric.nii.gz" ]; then
b_metrics="!(*afd*).nii.gz \${bname}_afd_metric.nii.gz"
else
b_metrics="$metrics"
b_metrics=($metrics)
if [[ -f \${bname}_afd_metric.nii.gz ]];
then
mv \${bname}_afd_metric.nii.gz afd_metric.nii.gz
b_metrics="\${b_metrics[@]//*afd_metric*}"
b_metrics+=" afd_metric.nii.gz"
fi

scil_compute_bundle_mean_std.py $density_weighting \$bname.trk \${b_metrics} >\
\${bname}.json
done
Expand Down Expand Up @@ -676,7 +682,7 @@ process Bundle_Volume_Per_Label {
metrics_for_mean_std_per_point
.mix(fixel_afd_for_mean_std_per_point)
.groupTuple(by: 0)
.map{it -> [it[0], it[1..-1].flatten()]}
.map{it -> [it[0], it[1..-1].flatten()]}
.set{metrics_afd_for_std_per_point}

metrics_afd_for_std_per_point
Expand Down Expand Up @@ -714,10 +720,12 @@ process Bundle_Mean_Std_Per_Point {
label_map=${sid}__\${bname}_labels.nii.gz
distance_map=${sid}__\${bname}_distances.nii.gz

if [ -f "\${bname}_afd_metric.nii.gz" ]; then
b_metrics="!(*afd*).nii.gz \${bname}_afd_metric.nii.gz"
else
b_metrics="$metrics"
b_metrics=($metrics)
if [[ -f \${bname}_afd_metric.nii.gz ]];
then
mv \${bname}_afd_metric.nii.gz afd_metric.nii.gz
b_metrics="\${b_metrics[@]//*afd_metric*}"
b_metrics+=" afd_metric.nii.gz"
fi

scil_compute_bundle_mean_std_per_point.py \$bname.trk \$label_map \
Expand Down Expand Up @@ -782,6 +790,7 @@ process Aggregate_All_Lesion_Load {
script:
"""
scil_merge_json.py $jsons lesion_load.json --average_last_layer --recursive
scil_harmonize_json.py lesion_load.json lesion_load.json -f -v --sort_keys
scil_convert_json_to_xlsx.py lesion_load.json lesion_load.xlsx
"""
}
Expand Down Expand Up @@ -809,6 +818,7 @@ process Aggregate_All_Lesion_Load_Per_Point {
done
scil_merge_json.py *_avg.json lesion_load_per_point.json \
--recursive
scil_harmonize_json.py lesion_load_per_point.json lesion_load_per_point.json -f -v --sort_keys
scil_convert_json_to_xlsx.py lesion_load_per_point.json lesion_load_per_point.xlsx \
--stats_over_population
"""
Expand All @@ -832,6 +842,7 @@ process Aggregate_All_Endpoints_Map {
script:
"""
scil_merge_json.py $jsons endpoints_map.json --no_list
scil_harmonize_json.py endpoints_map.json endpoints_map.json -f -v --sort_keys
scil_convert_json_to_xlsx.py endpoints_map.json endpoints_map.xlsx
"""
}
Expand All @@ -854,6 +865,7 @@ process Aggregate_All_Endpoints_Metric_Stats {
script:
"""
scil_merge_json.py $jsons endpoints_metric_stats.json --no_list
scil_harmonize_json.py endpoints_metric_stats.json endpoints_metric_stats.json -f -v --sort_keys
scil_convert_json_to_xlsx.py endpoints_metric_stats.json endpoints_metric_stats.xlsx
"""
}
Expand All @@ -876,6 +888,7 @@ process Aggregate_All_Bundle_Length_Stats {
script:
"""
scil_merge_json.py $jsons length_stats.json --no_list
scil_harmonize_json.py length_stats.json length_stats.json -f -v --sort_keys
scil_convert_json_to_xlsx.py length_stats.json length_stats.xlsx
"""
}
Expand All @@ -898,6 +911,7 @@ process Aggregate_All_mean_std {
script:
"""
scil_merge_json.py $jsons mean_std.json --no_list
scil_harmonize_json.py mean_std.json mean_std.json -f -v --sort_keys
scil_convert_json_to_xlsx.py mean_std.json mean_std.xlsx
"""
}
Expand All @@ -920,6 +934,7 @@ process Aggregate_All_Volume {
script:
"""
scil_merge_json.py $jsons volumes.json --no_list
scil_harmonize_json.py volumes.json volumes.json -f -v --sort_keys
scil_convert_json_to_xlsx.py volumes.json volumes.xlsx
"""
}
Expand All @@ -942,6 +957,7 @@ process Aggregate_All_Streamline_Count {
script:
"""
scil_merge_json.py $jsons streamline_count.json --no_list
scil_harmonize_json.py streamline_count.json streamline_count.json -f -v --sort_keys
scil_convert_json_to_xlsx.py streamline_count.json streamline_count.xlsx
"""
}
Expand All @@ -964,6 +980,7 @@ process Aggregate_All_Volume_Per_Label {
script:
"""
scil_merge_json.py $jsons volume_per_label.json --no_list
scil_harmonize_json.py volume_per_label.json volume_per_label.json -f -v --sort_keys
scil_convert_json_to_xlsx.py volume_per_label.json volume_per_label.xlsx
"""
}
Expand Down Expand Up @@ -991,6 +1008,7 @@ process Aggregate_All_Mean_Std_Per_Point {
done
scil_merge_json.py *_avg.json mean_std_per_point.json \
--recursive
scil_harmonize_json.py mean_std_per_point.json mean_std_per_point.json -f -v --sort_keys
scil_convert_json_to_xlsx.py mean_std_per_point.json mean_std_per_point.xlsx \
--stats_over_population
"""
Expand Down
3 changes: 0 additions & 3 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -19,9 +19,6 @@ params {
skip_projection_endpoints_metrics=true
bundle_suffix_to_remove='_cleaned'

min_streamline_count=100000
min_voxel_count=1000000

colors=["AC":"0x02d983",
"AF_L":"0xcc0000",
"AF_R":"0xffdf0f",
Expand Down