For the time being, since i have slicer installed in a computer which, by default, has no internet acess, i cannot download the sample data set and test TotalSegmentator with it. As soon as i have acess to internet, i will try.
The messages that appear after the Apply button are as follows:
Processing started
Writing input file to C:/Users/Augusto/AppData/Local/Temp/Slicer/__SlicerTemp__2022-12-15_21+10+39.789/total-segmentator-input.nii
Creating segmentations with TotalSegmentator AI…
Total Segmentator arguments: [‘-i’, ‘C:/Users/Augusto/AppData/Local/Temp/Slicer/__SlicerTemp__2022-12-15_21+10+39.789/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/Augusto/AppData/Local/Temp/Slicer/__SlicerTemp__2022-12-15_21+10+39.789/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]
If you have questions or suggestions, feel free to open an issue at GitHub - MIC-DKFZ/nnUNet
preprocessing C:\Users\Augusto\AppData\Local\Temp\nnunet_tmp_kqifjdkf\s01.nii.gz
before crop: (1, 228, 171, 171) after crop: (1, 228, 171, 171) spacing: [3. 3. 3.]
no resampling necessary
before: {‘spacing’: array([3., 3., 3.]), ‘spacing_transposed’: array([3., 3., 3.]), ‘data.shape (data is transposed)’: (1, 228, 171, 171)}
This worker has ended successfully, no errors to report
File “C:\Users\Augusto\AppData\Local\NA-MIC\Slicer 5.2.1\lib\Python\Scripts\TotalSegmentator”, line 201, in
File “C:\Users\Augusto\AppData\Local\NA-MIC\Slicer 5.2.1\lib\Python\Scripts\TotalSegmentator”, line 179, in main
File “C:\Users\Augusto\AppData\Local\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py”, line 232, in nnUNet_predict_image
File “C:\Users\Augusto\AppData\Local\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py”, line 106, in nnUNet_predict
File “C:\Users\Augusto\AppData\Local\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\nnunet\inference\predict.py”, line 668, in predict_from_folder
File “C:\Users\Augusto\AppData\Local\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\nnunet\inference\predict.py”, line 493, in predict_cases_fastest
File “C:\Users\Augusto\AppData\Local\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\nnunet\training\network_training\nnUNetTrainerV2.py”, line 211, in predict_preprocessed_data_return_seg_and_softmax
File “C:\Users\Augusto\AppData\Local\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\nnunet\training\network_training\nnUNetTrainer.py”, line 516, in predict_preprocessed_data_return_seg_and_softmax
File “C:\Users\Augusto\AppData\Local\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\nnunet\network_architecture\neural_network.py”, line 147, in predict_3D
File “C:\Users\Augusto\AppData\Local\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\nnunet\network_architecture\neural_network.py”, line 356, in _internal_predict_3D_3Dconv_tiled
RuntimeError: CUDA out of memory. Tried to allocate 1.30 GiB (GPU 0; 2.00 GiB total capacity; 120.31 MiB already allocated; 1.17 GiB free; 150.00 MiB reserved in total by PyTorch)
AttributeError: ‘DummyFile’ object has no attribute ‘flush’
Resampling…
Predicting…