# 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](https://github.com/wasserth/TotalSegmentator/) dataset and 372 from the [VerSe](https://github.com/anjany/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](https://github.com/MIC-DKFZ/nnUNet)) had problems in opening the images. The cases were identified by [others](https://github.com/wasserth/TotalSegmentator/issues/268) and through own analyses. Thus, these imaging studies were excluded.

``` python
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.

``` python
exclusion_missing_slices = ['tseg-s1018.nii.gz', 'tseg-s1063.nii.gz']
```