If there’s more than one input nii.gz file, then the operator adds _0001, _0002 and so on to the names of the extra files, as you can see below. Later it causes an error because the operator is missing the files with correct naming.
[2022-02-04 01:41:06,674] {pod_launcher.py:174} INFO - b'# Copy file /data/batch/1.3.12.2.1107.5.8.15.101357.30000021061115293388700002580/cropping-vertebrae/1.3.12.2.1107.5.8.15.101357.30000021061115293388700002580_15.nii.gz to /data/batch/1.3.12.2.1107.5.8.15.101357.30000021061115293388700002580/nnunet-input-data/1.3.12.2.1107.5.8.15.101357.30000021061115293388700002580_15_0000.nii.gz\n'
[2022-02-04 01:41:06,674] {pod_launcher.py:174} INFO - b'# Copy file /data/batch/1.3.12.2.1107.5.8.15.101357.30000021061115293388700002580/cropping-vertebrae/1.3.12.2.1107.5.8.15.101357.30000021061115293388700002580_10.nii.gz to /data/batch/1.3.12.2.1107.5.8.15.101357.30000021061115293388700002580/nnunet-input-data/1.3.12.2.1107.5.8.15.101357.30000021061115293388700002580_10_0001.nii.gz\n'
[2022-02-04 01:41:06,674] {pod_launcher.py:174} INFO - b'# Copy file /data/batch/1.3.12.2.1107.5.8.15.101357.30000021061115293388700002580/cropping-vertebrae/1.3.12.2.1107.5.8.15.101357.30000021061115293388700002580_16.nii.gz to /data/batch/1.3.12.2.1107.5.8.15.101357.30000021061115293388700002580/nnunet-input-data/1.3.12.2.1107.5.8.15.101357.30000021061115293388700002580_16_0002.nii.gz\n'