Processing started
Writing input file to C:/Users/96524/AppData/Local/Temp/Slicer/__SlicerTemp__2023-12-23_23+48+04.063/total-segmentator-input.nii
Creating segmentations with TotalSegmentator AI...
Total Segmentator arguments: ['-i', 'C:/Users/96524/AppData/Local/Temp/Slicer/__SlicerTemp__2023-12-23_23+48+04.063/total-segmentator-input.nii', '-o', 'C:/Users/96524/AppData/Local/Temp/Slicer/_SlicerTemp__2023-12-23_23+48+04.063/segmentation', '--ml', '--task', 'total', '--fast']
C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Lib\site-packages\requests_init.py:102: RequestsDependencyWarning: urllib3 (1.26.12) or chardet (5.0.0)/charset_normalizer (2.0.12) doesn't match a supported version!
warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "
Traceback (most recent call last):
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Scripts\TotalSegmentator", line 93, in
main()
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Scripts\TotalSegmentator", line 86, in main
totalsegmentator(args.input, args.output, args.ml, args.nr_thr_resamp, args.nr_thr_saving,
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Lib\site-packages\totalsegmentator\python_api.py", line 173, in totalsegmentator
seg = nnUNet_predict_image(input, output, task_id, model=model, folds=folds,
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py", line 255, in nnUNet_predict_image
nnUNet_predict(tmp_dir, tmp_dir, task_id, model, folds, trainer, tta)
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py", line 106, in nnUNet_predict
predict_from_folder(model_folder_name, dir_in, dir_out, folds, save_npz, num_threads_preprocessing,
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Lib\site-packages\nnunet\inference\predict.py", line 616, in predict_from_folder
shutil.copy(join(model, 'plans.pkl'), output_folder)
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Lib\shutil.py", line 427, in copy
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Lib\shutil.py", line 264, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: 'C:\Users\96524\.totalsegmentator\nnunet\results\nnUNet\3d_fullres\Task256_TotalSegmentator_3mm_1139subj\nnUNetTrainerV2_ep8000_nomirror__nnUNetPlansv2.1\plans.pkl'
Exception ignored in: <totalsegmentator.libs.DummyFile object at 0x0000015CA1C56C40>
AttributeError: 'DummyFile' object has no attribute 'flush'
Processing started
Writing input file to C:/Users/96524/AppData/Local/Temp/Slicer/__SlicerTemp__2023-12-23_23+48+04.063/total-segmentator-input.nii
Creating segmentations with TotalSegmentator AI...
Total Segmentator arguments: ['-i', 'C:/Users/96524/AppData/Local/Temp/Slicer/__SlicerTemp__2023-12-23_23+48+04.063/total-segmentator-input.nii', '-o', 'C:/Users/96524/AppData/Local/Temp/Slicer/_SlicerTemp__2023-12-23_23+48+04.063/segmentation', '--ml', '--task', 'total', '--fast']
C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Lib\site-packages\requests_init.py:102: RequestsDependencyWarning: urllib3 (1.26.12) or chardet (5.0.0)/charset_normalizer (2.0.12) doesn't match a supported version!
warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "
Traceback (most recent call last):
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Scripts\TotalSegmentator", line 93, in
main()
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Scripts\TotalSegmentator", line 86, in main
totalsegmentator(args.input, args.output, args.ml, args.nr_thr_resamp, args.nr_thr_saving,
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Lib\site-packages\totalsegmentator\python_api.py", line 173, in totalsegmentator
seg = nnUNet_predict_image(input, output, task_id, model=model, folds=folds,
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py", line 255, in nnUNet_predict_image
nnUNet_predict(tmp_dir, tmp_dir, task_id, model, folds, trainer, tta)
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py", line 106, in nnUNet_predict
predict_from_folder(model_folder_name, dir_in, dir_out, folds, save_npz, num_threads_preprocessing,
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Lib\site-packages\nnunet\inference\predict.py", line 616, in predict_from_folder
shutil.copy(join(model, 'plans.pkl'), output_folder)
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Lib\shutil.py", line 427, in copy
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "C:\Users\96524\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-30\lib\Python\Lib\shutil.py", line 264, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: 'C:\Users\96524\.totalsegmentator\nnunet\results\nnUNet\3d_fullres\Task256_TotalSegmentator_3mm_1139subj\nnUNetTrainerV2_ep8000_nomirror__nnUNetPlansv2.1\plans.pkl'
Exception ignored in: <totalsegmentator.libs.DummyFile object at 0x0000015CA1C56C40>
AttributeError: 'DummyFile' object has no attribute 'flush'