Exclusions
Due to non-orthogonal direction matrices or missing slices, 142 patients were exluded from further labeling. The final dataset consists of 1460 computed tomography images and associated labels of the vertebral bodies, 1088 from the TotalSegmentator dataset and 372 from the VerSe dataset.
Non-Orthogonal Direction Matrix
In 140 cases, the direction matrix was non-orthogonal and the ITK tool (e.g. used by nnU-Net) had problems in opening the images. The cases were identified by others and through own analyses. Thus, these imaging studies were excluded.
exclusion_non_orthogonal = ['tseg-s0000.nii.gz', 'tseg-s0001.nii.gz', 'tseg-s0002.nii.gz', 'tseg-s0004.nii.gz', 'tseg-s0025.nii.gz', 'tseg-s0043.nii.gz', 'tseg-s0048.nii.gz', 'tseg-s0061.nii.gz', 'tseg-s0062.nii.gz', 'tseg-s0066.nii.gz', 'tseg-s0067.nii.gz', 'tseg-s0079.nii.gz', 'tseg-s0081.nii.gz', 'tseg-s0090.nii.gz', 'tseg-s0107.nii.gz', 'tseg-s0112.nii.gz', 'tseg-s0114.nii.gz', 'tseg-s0117.nii.gz', 'tseg-s0130.nii.gz', 'tseg-s0146.nii.gz', 'tseg-s0149.nii.gz', 'tseg-s0154.nii.gz', 'tseg-s0169.nii.gz', 'tseg-s0189.nii.gz', 'tseg-s0193.nii.gz', 'tseg-s0208.nii.gz', 'tseg-s0209.nii.gz', 'tseg-s0226.nii.gz', 'tseg-s0235.nii.gz', 'tseg-s0236.nii.gz', 'tseg-s0242.nii.gz', 'tseg-s0254.nii.gz', 'tseg-s0278.nii.gz', 'tseg-s0282.nii.gz', 'tseg-s0295.nii.gz', 'tseg-s0299.nii.gz', 'tseg-s0301.nii.gz', 'tseg-s0311.nii.gz', 'tseg-s0326.nii.gz', 'tseg-s0352.nii.gz', 'tseg-s0353.nii.gz', 'tseg-s0361.nii.gz', 'tseg-s0386.nii.gz', 'tseg-s0396.nii.gz', 'tseg-s0417.nii.gz', 'tseg-s0436.nii.gz', 'tseg-s0457.nii.gz', 'tseg-s0462.nii.gz', 'tseg-s0493.nii.gz', 'tseg-s0504.nii.gz', 'tseg-s0514.nii.gz', 'tseg-s0526.nii.gz', 'tseg-s0527.nii.gz', 'tseg-s0552.nii.gz', 'tseg-s0557.nii.gz', 'tseg-s0559.nii.gz', 'tseg-s0561.nii.gz', 'tseg-s0563.nii.gz', 'tseg-s0585.nii.gz', 'tseg-s0611.nii.gz', 'tseg-s0614.nii.gz', 'tseg-s0622.nii.gz', 'tseg-s0624.nii.gz', 'tseg-s0625.nii.gz', 'tseg-s0647.nii.gz', 'tseg-s0648.nii.gz', 'tseg-s0684.nii.gz', 'tseg-s0700.nii.gz', 'tseg-s0712.nii.gz', 'tseg-s0735.nii.gz', 'tseg-s0737.nii.gz', 'tseg-s0740.nii.gz', 'tseg-s0744.nii.gz', 'tseg-s0751.nii.gz', 'tseg-s0759.nii.gz', 'tseg-s0768.nii.gz', 'tseg-s0770.nii.gz', 'tseg-s0772.nii.gz', 'tseg-s0774.nii.gz', 'tseg-s0776.nii.gz', 'tseg-s0783.nii.gz', 'tseg-s0795.nii.gz', 'tseg-s0802.nii.gz', 'tseg-s0805.nii.gz', 'tseg-s0806.nii.gz', 'tseg-s0808.nii.gz', 'tseg-s0809.nii.gz', 'tseg-s0816.nii.gz', 'tseg-s0829.nii.gz', 'tseg-s0833.nii.gz', 'tseg-s0837.nii.gz', 'tseg-s0843.nii.gz', 'tseg-s0844.nii.gz', 'tseg-s0845.nii.gz', 'tseg-s0860.nii.gz', 'tseg-s0867.nii.gz', 'tseg-s0874.nii.gz', 'tseg-s0909.nii.gz', 'tseg-s0910.nii.gz', 'tseg-s0930.nii.gz', 'tseg-s0944.nii.gz', 'tseg-s0949.nii.gz', 'tseg-s0976.nii.gz', 'tseg-s0978.nii.gz', 'tseg-s0982.nii.gz', 'tseg-s0986.nii.gz', 'tseg-s1000.nii.gz', 'tseg-s1005.nii.gz', 'tseg-s1009.nii.gz', 'tseg-s1011.nii.gz', 'tseg-s1023.nii.gz', 'tseg-s1035.nii.gz', 'tseg-s1038.nii.gz', 'tseg-s1040.nii.gz', 'tseg-s1046.nii.gz', 'tseg-s1050.nii.gz', 'tseg-s1083.nii.gz', 'tseg-s1103.nii.gz', 'tseg-s1133.nii.gz', 'tseg-s1141.nii.gz', 'tseg-s1147.nii.gz', 'tseg-s1148.nii.gz', 'tseg-s1170.nii.gz', 'tseg-s1174.nii.gz', 'tseg-s1205.nii.gz', 'tseg-s1234.nii.gz', 'tseg-s1235.nii.gz', 'tseg-s1237.nii.gz', 'tseg-s1272.nii.gz', 'tseg-s1276.nii.gz', 'tseg-s1295.nii.gz', 'tseg-s1344.nii.gz', 'tseg-s1389.nii.gz', 'tseg-s1406.nii.gz', 'tseg-s1407.nii.gz', 'tseg-s1409.nii.gz', 'tseg-s1417.nii.gz', 'tseg-s1419.nii.gz', 'verse-700.nii.gz', 'verse-813.nii.gz']
Missing slices
In two patients from the TotalSegmentator dataset, images had missing slices. Thus, these patients were excluded from both, the training and the validation dataset.
exclusion_missing_slices = ['tseg-s1018.nii.gz', 'tseg-s1063.nii.gz']