Keyword=CombinedLabels incompatible with combine=1

[jcohenadad]

Context

When running sct_extract_metric with a combination the flag -l that points to a label Keyword=CombinedLabels, i.e., with values 50 to 55, while using the flag -combine 1, the script crashes:

/results_20240503_134220/data_processed/sub-BB277/dwi $  /usr/bin/env /Users/julien/code/spinalcordtoolbox/python/bin/python /Users/julien/.vscode/extensions/ms-python.python-2024.4.1/python_files/lib/python/debugpy/adapter/../../debugpy/launcher 50935 -- /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_extract_metric.py -i sub-BB277_chunk-1_DWI_moco_FA.nii.gz -f label_sub-BB277_chunk-1_DWI_moco/atlas -l 52 -combine 1 -vert 2:12 -vertfile label_sub-BB277_chunk-1_DWI_moco/template/PAM50_levels.nii.gz -o /Users/julien/code/spine-park/results_20240503_134220/results/DWI_FA_52.csv 

--
Spinal Cord Toolbox (git-jca/extract-metric-combine-72ff27030efda92431ee831b45f31e2858b8552d)

sct_extract_metric -i sub-BB277_chunk-1_DWI_moco_FA.nii.gz -f label_sub-BB277_chunk-1_DWI_moco/atlas -l 52 -combine 1 -vert 2:12 -vertfile label_sub-BB277_chunk-1_DWI_moco/template/PAM50_levels.nii.gz -o /Users/julien/code/spine-park/results_20240503_134220/results/DWI_FA_52.csv
--


Load metric image...
Estimation for label: 52
Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_extract_metric.py", line 390, in <module>
    main(sys.argv[1:])
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_extract_metric.py", line 379, in main
    agg_metric = extract_metric(data, labels=labels, slices=slices, levels=levels, perslice=perslice,
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/aggregate_slicewise.py", line 440, in extract_metric
    labels_sum = np.sum(labels[..., label_struc[id_label].id], axis=labels.ndim-1)  # (nx, ny, nz, 1)
IndexError: index 52 is out of bounds for axis 3 with size 37

While when setting combine 0, the script runs:

julien-macbook:~/code/spine-park/results_20240503_134220/data_processed/sub-BB277/dwi $  cd /Users/julien/code/spine-park/results_20240503_134220/data_processed/sub-BB277/dwi ; /usr/bin/env /Users/julien/code/spinalcordtoolbox/python/bin/python /Users/julien/.vscode/extensions/ms-python.python-2024.4.1/python_files/lib/python/debugpy/adapter/../../debugpy/launcher 50940 -- /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_extract_metric.py -i sub-BB277_chunk-1_DWI_moco_FA.nii.gz -f label_sub-BB277_chunk-1_DWI_moco/atlas -l 52 -combine 0 -vert 2:12 -vertfile label_sub-BB277_chunk-1_DWI_moco/template/PAM50_levels.nii.gz -o /Users/julien/code/spine-park/results_20240503_134220/results/DWI_FA_52.csv 

--
Spinal Cord Toolbox (git-jca/extract-metric-combine-72ff27030efda92431ee831b45f31e2858b8552d)

sct_extract_metric -i sub-BB277_chunk-1_DWI_moco_FA.nii.gz -f label_sub-BB277_chunk-1_DWI_moco/atlas -l 52 -combine 0 -vert 2:12 -vertfile label_sub-BB277_chunk-1_DWI_moco/template/PAM50_levels.nii.gz -o /Users/julien/code/spine-park/results_20240503_134220/results/DWI_FA_52.csv
--


Load metric image...
Estimation for label: gray matter

Done! To view results, type:
open /Users/julien/code/spine-park/results_20240503_134220/results/DWI_FA_52.csv

Although it does not really make sense to combine tracts that are already combined, this crash is not intuitive for the user.

Solution

Deal with the condition 'CombinedLabel' & combine=1.