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Add sagittal mosaic images to sample #36

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Merged
elhil merged 1 commit into from
Mar 2, 2026
Merged

Add sagittal mosaic images to sample #36

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Binary file added ...ata/sct_example_data/t2/sct_deepseg/2025_03_07_100540.073184/background_img.png
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Binary file added ...t/data/sct_example_data/t2/sct_deepseg/2025_03_07_100540.073184/overlay_img.png
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54 changes: 35 additions & 19 deletions sample/default/js/datasets.js
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Original file line number Diff line number Diff line change
@@ -1,10 +1,26 @@
window.SCT_QC_UUID = 'd4ac2e7d-74c7-438e-a544-9c71023730a5';
window.SCT_QC_DATASETS = [
{
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/t2",
"cmdline": "sct_deepseg -i t2_fake_lesion.nii.gz -task seg_sc_lesion_t2w_sci -o t2_deepseg.nii.gz -qc /path/to/spinalcordtoolbox/qc_example_data -qc-plane Sagittal -qc-seg t2_fake_lesion_sc_seg.nii.gz",
"command": "sct_deepseg",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "t2",
"inputFile": "t2_fake_lesion.nii.gz",
"plane": "Sagittal",
"backgroundImage": "sample/default/data/sct_example_data/t2/sct_deepseg/2025_03_07_100540.073184/background_img.png",
"overlayImage": "sample/default/data/sct_example_data/t2/sct_deepseg/2025_03_07_100540.073184/overlay_img.png",
"date": "2025-03-07 10:05:40",
"rank": "",
"qc": ""
},
{
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/t2",
"cmdline": "sct_deepseg_sc -i t2.nii.gz -c t2 -qc /path/to/spinalcordtoolbox/qc_example_data",
"command": "sct_deepseg_sc",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "t2",
Expand All @@ -20,7 +36,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/t2",
"cmdline": "sct_get_centerline -i t2_seg.nii.gz -method fitseg -qc /path/to/spinalcordtoolbox/qc_example_data",
"command": "sct_get_centerline",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "t2",
Expand All @@ -36,7 +52,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/t2",
"cmdline": "sct_get_centerline -i t2_seg.nii.gz -method fitseg -centerline-soft 1 -o t2_seg_centerline_soft.nii.gz -qc /path/to/spinalcordtoolbox/qc_example_data",
"command": "sct_get_centerline",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "t2",
Expand All @@ -52,7 +68,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/t2",
"cmdline": "sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -qc /path/to/spinalcordtoolbox/qc_example_data",
"command": "sct_label_vertebrae",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "t2",
Expand All @@ -68,7 +84,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/t2",
"cmdline": "sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l labels_vert.nii.gz -c t2 -qc /path/to/spinalcordtoolbox/qc_example_data",
"command": "sct_register_to_template",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "t2",
Expand All @@ -84,7 +100,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/t2",
"cmdline": "sct_detect_pmj -i t2.nii.gz -c t2 -qc /path/to/spinalcordtoolbox/qc_example_data",
"command": "sct_detect_pmj",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "t2",
Expand All @@ -100,7 +116,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/t2",
"cmdline": "sct_process_segmentation -i t2_seg.nii.gz -pmj t2_pmj.nii.gz -pmj-distance 60 -pmj-extent 30 -qc /path/to/spinalcordtoolbox/qc_example_data -qc-image t2.nii.gz -o csa_pmj.csv",
"command": "sct_process_segmentation",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "t2",
Expand All @@ -116,7 +132,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/t2s",
"cmdline": "sct_deepseg_sc -i t2s.nii.gz -c t2s -qc /path/to/spinalcordtoolbox/qc_example_data",
"command": "sct_deepseg_sc",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "t2s",
Expand All @@ -132,7 +148,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/t2s",
"cmdline": "sct_deepseg_gm -i t2s.nii.gz -qc /path/to/spinalcordtoolbox/qc_example_data",
"command": "sct_deepseg_gm",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "t2s",
Expand All @@ -148,7 +164,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/mt",
"cmdline": "sct_deepseg_sc -i mt1_crop.nii.gz -c t2 -qc /path/to/spinalcordtoolbox/qc_example_data",
"command": "sct_deepseg_sc",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "mt",
Expand All @@ -164,7 +180,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/mt",
"cmdline": "sct_register_multimodal -i mt0.nii.gz -d mt1_crop.nii.gz -dseg mt1_crop_seg.nii.gz -param step=1,type=im,algo=slicereg,metric=CC -x spline -qc /path/to/spinalcordtoolbox/qc_example_data",
"command": "sct_register_multimodal",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "mt",
Expand All @@ -180,7 +196,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/mt",
"cmdline": "sct_warp_template -d mt1_crop.nii.gz -w warp_template2mt.nii.gz -qc /path/to/spinalcordtoolbox/qc_example_data",
"command": "sct_warp_template",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "mt",
Expand All @@ -196,7 +212,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/mt",
"cmdline": "sct_register_multimodal -i t1w.nii.gz -d mt1_crop.nii.gz -dseg mt1_crop_seg.nii.gz -param step=1,type=im,algo=slicereg,metric=CC -x spline -qc /path/to/spinalcordtoolbox/qc_example_data",
"command": "sct_register_multimodal",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "mt",
Expand All @@ -212,7 +228,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/dmri",
"cmdline": "sct_deepseg_sc -i dmri_moco_dwi_mean.nii.gz -c dwi -qc /path/to/spinalcordtoolbox/qc_example_data",
"command": "sct_deepseg_sc",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "dmri",
Expand All @@ -228,7 +244,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/dmri",
"cmdline": "sct_dmri_moco (\"sct_qc -i dmri.nii.gz -d dmri_moco.nii.gz -s dmri_moco_dwi_mean_seg.nii.gz -p sct_dmri_moco -qc /path/to/spinalcordtoolbox/qc_example_data\")",
"command": "sct_dmri_moco",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "dmri",
Expand All @@ -244,7 +260,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/dmri",
"cmdline": "sct_register_multimodal -i /path/to/spinalcordtoolbox/data/PAM50/template/PAM50_t1.nii.gz -iseg /path/to/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz -d dmri_moco_dwi_mean.nii.gz -dseg dmri_moco_dwi_mean_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,smooth=1,iter=3 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -qc /path/to/spinalcordtoolbox/qc_example_data -owarp warp_template2dmri.nii.gz -owarpinv warp_dmri2template.nii.gz",
"command": "sct_register_multimodal",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "dmri",
Expand All @@ -260,7 +276,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/dmri",
"cmdline": "sct_warp_template -d dmri_moco_dwi_mean.nii.gz -w warp_template2dmri.nii.gz -qc /path/to/spinalcordtoolbox/qc_example_data",
"command": "sct_warp_template",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "dmri",
Expand All @@ -276,7 +292,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/fmri",
"cmdline": "sct_fmri_moco (\"sct_qc -i fmri.nii.gz -d fmri_moco.nii.gz -s fmri_crop_moco_mean_seg_manual.nii.gz -p sct_fmri_moco -qc /path/to/spinalcordtoolbox/qc_example_data\")",
"command": "sct_fmri_moco",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "fmri",
Expand All @@ -292,7 +308,7 @@ window.SCT_QC_DATASETS = [
"path": "/path/to/spinalcordtoolbox/data/sct_example_data/fmri",
"cmdline": "sct_register_multimodal -i /path/to/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz -iseg /path/to/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz -d fmri_moco_mean.nii.gz -dseg fmri_crop_moco_mean_seg_manual.nii.gz -param step=1,type=seg,algo=slicereg,metric=MeanSquares,smooth=2:step=2,type=im,algo=bsplinesyn,metric=MeanSquares,iter=5,gradStep=0.5 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -qc /path/to/spinalcordtoolbox/qc_example_data -owarp warp_template2fmri.nii.gz -owarpinv warp_fmri2template.nii.gz",
"command": "sct_register_multimodal",
"sctVersion": "git-master-192c518c829a7d8ea7764a63c4b46748ff2ed836",
"sctVersion": "v7.1",
"dataset": "data",
"subject": "sct_example_data",
"contrast": "fmri",
Expand Down