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wasserth / TotalSegmentator

Tool for robust segmentation of >100 important anatomical structures in CT and MR images
Apache License 2.0
1.48k stars 246 forks source link

Is this downloading in fast mode itended ? it happens every time. #196

Closed rbumm closed 1 year ago

rbumm commented 1 year ago 
  0%|          | 0/8 [00:00<?, ?it/s]
 12%|#2        | 1/8 [00:01<00:07,  1.13s/it]
100%|##########| 8/8 [00:01<00:00,  6.85it/s]

Best Rudolf

wasserth commented 1 year ago

For me it does only download weights once. On consecutive calls it does not happen. Can you paste the entire output here? Do you run it from the command line or from within slicer?

rbumm commented 1 year ago

This is the full output running TotalSegmentator from 3D Slicer without FAST mode. 0% to 100 % several times, looks like a download, and it happens every time again when I restart the procedure. 

Processing started
Writing input file to C:/Users/Rudolf/AppData/Local/Temp/Slicer/__SlicerTemp__2023-10-16_11+33+23.285/total-segmentator-input.nii
Creating segmentations with TotalSegmentator AI...
Total Segmentator arguments: ['-i', 'C:/Users/Rudolf/AppData/Local/Temp/Slicer/__SlicerTemp__2023-10-16_11+33+23.285/total-segmentator-input.nii', '-o', 'C:/Users/Rudolf/AppData/Local/Temp/Slicer/__SlicerTemp__2023-10-16_11+33+23.285/segmentation', '--ml', '--task', 'total']
C:\Users\Rudolf\AppData\Local\slicer.org\Slicer 5.4.0_2\lib\Python\Lib\site-packages\requests\__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.17) or chardet (5.1.0)/charset_normalizer (2.0.12) doesn't match a supported version!
  warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "
C:\Users\Rudolf\AppData\Local\slicer.org\Slicer 5.4.0_2\lib\Python\Lib\site-packages\requests\__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.17) or chardet (5.1.0)/charset_normalizer (2.0.12) doesn't match a supported version!
  warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "

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C:\Users\Rudolf\AppData\Local\slicer.org\Slicer 5.4.0_2\lib\Python\Lib\site-packages\requests\__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.17) or chardet (5.1.0)/charset_normalizer (2.0.12) doesn't match a supported version!
  warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "
C:\Users\Rudolf\AppData\Local\slicer.org\Slicer 5.4.0_2\lib\Python\Lib\site-packages\requests\__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.17) or chardet (5.1.0)/charset_normalizer (2.0.12) doesn't match a supported version!
  warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "

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C:\Users\Rudolf\AppData\Local\slicer.org\Slicer 5.4.0_2\lib\Python\Lib\site-packages\requests\__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.17) or chardet (5.1.0)/charset_normalizer (2.0.12) doesn't match a supported version!
  warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "
C:\Users\Rudolf\AppData\Local\slicer.org\Slicer 5.4.0_2\lib\Python\Lib\site-packages\requests\__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.17) or chardet (5.1.0)/charset_normalizer (2.0.12) doesn't match a supported version!
  warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "

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C:\Users\Rudolf\AppData\Local\slicer.org\Slicer 5.4.0_2\lib\Python\Lib\site-packages\requests\__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.17) or chardet (5.1.0)/charset_normalizer (2.0.12) doesn't match a supported version!
  warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "
C:\Users\Rudolf\AppData\Local\slicer.org\Slicer 5.4.0_2\lib\Python\Lib\site-packages\requests\__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.17) or chardet (5.1.0)/charset_normalizer (2.0.12) doesn't match a supported version!
  warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "

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C:\Users\Rudolf\AppData\Local\slicer.org\Slicer 5.4.0_2\lib\Python\Lib\site-packages\requests\__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.17) or chardet (5.1.0)/charset_normalizer (2.0.12) doesn't match a supported version!
  warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "
C:\Users\Rudolf\AppData\Local\slicer.org\Slicer 5.4.0_2\lib\Python\Lib\site-packages\requests\__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.17) or chardet (5.1.0)/charset_normalizer (2.0.12) doesn't match a supported version!
  warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "

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C:\Users\Rudolf\AppData\Local\slicer.org\Slicer 5.4.0_2\lib\Python\Lib\site-packages\requests\__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.17) or chardet (5.1.0)/charset_normalizer (2.0.12) doesn't match a supported version!
  warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "

If you use this tool please cite: https://pubs.rsna.org/doi/10.1148/ryai.230024

Resampling...
  Resampled in 6.84s
Predicting part 1 of 5 ...
Predicting part 2 of 5 ...
Predicting part 3 of 5 ...
Predicting part 4 of 5 ...
Predicting part 5 of 5 ...
  Predicted in 260.77s
Resampling...
Saving segmentations...
  Saved in 0.69s
Importing segmentation results...
Failed to deserialize terminology string: Segmentation category and type - Total Segmentator~SCT^123037004^Anatomical Structure~SCT^69748006^Thyroid structure~SCT^^~Anatomic codes - DICOM master list~^^~^^|
Failed to deserialize terminology string: Segmentation category and type - DICOM master list~SCT^123037004^Anatomical Structure~SCT^53603007^Entire pulmonary vein~^^~Anatomic codes - DICOM master list~^^~^^|
Failed to deserialize terminology string: Segmentation category and type - Total Segmentator~SCT^123037004^Anatomical Structure~SCT^29700009^Subclavian artery~SCT^24028007^Right~Anatomic codes - DICOM master list~^^~^^|
Failed to deserialize terminology string: Segmentation category and type - Total Segmentator~SCT^123037004^Anatomical Structure~SCT^85235006^Subclavian artery~SCT^7771000^Left~Anatomic codes - DICOM master list~^^~^^|
Failed to deserialize terminology string: Segmentation category and type - Total Segmentator~SCT^123037004^Anatomical Structure~SCT^65355003^Right common carotid artery~SCT^24028007^Right~Anatomic codes - DICOM master list~^^~^^|
Failed to deserialize terminology string: Segmentation category and type - Total Segmentator~SCT^123037004^Anatomical Structure~SCT^113263003^Left common carotid artery~SCT^7771000^Left~Anatomic codes - DICOM master list~^^~^^|
Failed to deserialize terminology string: Segmentation category and type - Total Segmentator~SCT^123037004^Anatomical Structure~SCT^8887007^Brachiocephalic vein~SCT^7771000^Left~Anatomic codes - DICOM master list~^^~^^|
Failed to deserialize terminology string: Segmentation category and type - Total Segmentator~SCT^123037004^Anatomical Structure~SCT^8887007^Brachiocephalic vein~SCT^24028007^Right~Anatomic codes - DICOM master list~^^~^^|
Failed to deserialize terminology string: Segmentation category and type - DICOM master list~SCT^123037004^Anatomical Structure~SCT^305223006^Entire atrial appendage~^7771000^Left~Anatomic codes - DICOM master list~^^~^^|
Failed to deserialize terminology string: Segmentation category and type - Total Segmentator~SCT^123037004^Anatomical Structure~SCT^ 50016007^Rib cartilage~SCT^^Anatomic codes - DICOM master list~^^~^^|
Cleaning up temporary folder...
Processing completed in 296.09 seconds

Processing finished.
wasserth commented 1 year ago

I guess in Slicer it does not recognize the downloaded weights. How do you specify in Slicer where the weights are stored? Do you set TOTALSEG_WEIGHTS_PATH ? Or do you not specify anything and they get stored to a default location?

rbumm commented 1 year ago

TOTALSEG_WEIGHTS_PATH was not set, but I also tried setting that environment variable (pointing it to the Slicer script directory). What is the name of the weight file file that should be generated?

wasserth commented 1 year ago

For v2.0.3: The default TOTALSEG_WEIGHTS_PATH is ~/.totalsegmentator/nnunet/results and for the fast model it should download the file Dataset297_TotalSegmentator_total_3mm_1559subj.zip into this directory and extract it. In v2.0.4 the filename has changed slightly to Dataset297_TotalSegmentator_total_3mm_1559subj_v204.zip.

rbumm commented 1 year ago

I found the downloaded file in the .totalsegmentator directory of my user dir, it is unzipped, but it gets redownloaded upon every application ot Totalsegmentator by 3D Slicer. The folder is not protected. .

[image: image.png]

Am Do., 19. Okt. 2023 um 13:15 Uhr schrieb Jakob Wasserthal < @.***>:

For v2.0.3: The default TOTALSEG_WEIGHTS_PATH is ~/.totalsegmentator/nnunet/results and for the fast model it should download the file Dataset297_TotalSegmentator_total_3mm_1559subj.zip into this directory and extract it. In v2.0.4 the filename has changed slightly to Dataset297_TotalSegmentator_total_3mm_1559subj_v204.zip.

— Reply to this email directly, view it on GitHub https://github.com/wasserth/TotalSegmentator/issues/196#issuecomment-1770653066, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEKMXPVFOMETJW3C7SVBNH3YAEDTRAVCNFSM6AAAAAA6ATWYPSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONZQGY2TGMBWGY . You are receiving this because you authored the thread.Message ID: @.***>

rbumm commented 1 year ago

It is a folder, not a file, with several subfolders.

Am Do., 19. Okt. 2023 um 15:30 Uhr schrieb Rudolf B < @.***>:

I found the downloaded file in the .totalsegmentator directory of my user dir, it is unzipped, but it gets redownloaded upon every application ot Totalsegmentator by 3D Slicer. The folder is not protected. .

[image: image.png]

Am Do., 19. Okt. 2023 um 13:15 Uhr schrieb Jakob Wasserthal < @.***>:

For v2.0.3: The default TOTALSEG_WEIGHTS_PATH is ~/.totalsegmentator/nnunet/results and for the fast model it should download the file Dataset297_TotalSegmentator_total_3mm_1559subj.zip into this directory and extract it. In v2.0.4 the filename has changed slightly to Dataset297_TotalSegmentator_total_3mm_1559subj_v204.zip.

— Reply to this email directly, view it on GitHub https://github.com/wasserth/TotalSegmentator/issues/196#issuecomment-1770653066, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEKMXPVFOMETJW3C7SVBNH3YAEDTRAVCNFSM6AAAAAA6ATWYPSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONZQGY2TGMBWGY . You are receiving this because you authored the thread.Message ID: @.***>

wasserth commented 1 year ago

Correct, it should be a folder with subfolders. I do not really have an idea why it is getting downloaded over and over again :|

lassoan commented 1 year ago

@rbumm I see these progress bars, but I'm not sure if they refer to downloading or just feedback for some processing:

Processing started
Writing input file to C:/Users/andra/AppData/Local/Temp/Slicer/__SlicerTemp__2023-10-19_09+45+37.921/total-segmentator-input.nii
Creating segmentations with TotalSegmentator AI...
Total Segmentator arguments: ['-i', 'C:/Users/andra/AppData/Local/Temp/Slicer/__SlicerTemp__2023-10-19_09+45+37.921/total-segmentator-input.nii', '-o', 'C:/Users/andra/AppData/Local/Temp/Slicer/__SlicerTemp__2023-10-19_09+45+37.921/segmentation', '--ml', '--task', 'total']

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 44%|####4     | 16/36 [00:02<00:02,  9.03it/s]
 61%|######1   | 22/36 [00:02<00:01,  9.95it/s]
 72%|#######2  | 26/36 [00:03<00:00, 10.30it/s]
 81%|########  | 29/36 [00:03<00:00, 10.61it/s]
 89%|########8 | 32/36 [00:03<00:00, 10.87it/s]
 94%|#########4| 34/36 [00:03<00:00, 10.99it/s]
100%|##########| 36/36 [00:04<00:00, 11.13it/s]
100%|##########| 36/36 [00:04<00:00,  8.78it/s]

  0%|          | 0/36 [00:00<?, ?it/s]
 33%|###3      | 12/36 [00:00<00:00, 117.65it/s]
 67%|######6   | 24/36 [00:00<00:00, 23.25it/s]
 83%|########3 | 30/36 [00:01<00:00, 17.87it/s]
 94%|#########4| 34/36 [00:01<00:00, 16.17it/s]
100%|##########| 36/36 [00:01<00:00, 18.62it/s]

  0%|          | 0/36 [00:00<?, ?it/s]
 39%|###8      | 14/36 [00:00<00:00, 138.61it/s]
 78%|#######7  | 28/36 [00:01<00:00, 20.15it/s]
 97%|#########7| 35/36 [00:01<00:00, 16.23it/s]
100%|##########| 36/36 [00:01<00:00, 18.72it/s]

  0%|          | 0/36 [00:00<?, ?it/s]
 39%|###8      | 14/36 [00:00<00:00, 66.99it/s]
 58%|#####8    | 21/36 [00:00<00:00, 22.58it/s]
 69%|######9   | 25/36 [00:01<00:00, 18.48it/s]
 78%|#######7  | 28/36 [00:01<00:00, 16.51it/s]
 83%|########3 | 30/36 [00:01<00:00, 15.72it/s]
 89%|########8 | 32/36 [00:01<00:00, 14.99it/s]
 94%|#########4| 34/36 [00:01<00:00, 14.14it/s]
100%|##########| 36/36 [00:02<00:00, 13.78it/s]
100%|##########| 36/36 [00:02<00:00, 17.69it/s]

  0%|          | 0/36 [00:00<?, ?it/s]
 39%|###8      | 14/36 [00:00<00:00, 100.00it/s]
 67%|######6   | 24/36 [00:01<00:00, 20.29it/s]
 81%|########  | 29/36 [00:01<00:00, 17.10it/s]
 92%|#########1| 33/36 [00:01<00:00, 15.66it/s]
100%|##########| 36/36 [00:02<00:00, 14.97it/s]
100%|##########| 36/36 [00:02<00:00, 18.00it/s]

If you use this tool please cite: https://pubs.rsna.org/doi/10.1148/ryai.230024

Resampling...
  Resampled in 10.76s
Predicting part 1 of 5 ...
Predicting part 2 of 5 ...
Predicting part 3 of 5 ...
Predicting part 4 of 5 ...
Predicting part 5 of 5 ...
  Predicted in 104.88s
Resampling...
Saving segmentations...
  Saved in 3.18s
Importing segmentation results...
Cleaning up temporary folder...
Processing completed in 147.69 seconds

Processing finished.
rbumm commented 1 year ago

Could you shed some light on that Jakob?Sent from my iPhoneOn 19 Oct 2023, at 15:50, Andras Lasso @.***> wrote: @rbumm I see these progress bars, but I'm not sure if they refer to downloading or just feedback for some processing: Processing started Writing input file to C:/Users/andra/AppData/Local/Temp/Slicer/SlicerTemp2023-10-19_09+45+37.921/total-segmentator-input.nii Creating segmentations with TotalSegmentator AI... Total Segmentator arguments: ['-i', 'C:/Users/andra/AppData/Local/Temp/Slicer/SlicerTemp2023-10-19_09+45+37.921/total-segmentator-input.nii', '-o', 'C:/Users/andra/AppData/Local/Temp/Slicer/SlicerTemp2023-10-19_09+45+37.921/segmentation', '--ml', '--task', 'total']

0%| | 0/36 [00:00<?, ?it/s] 3%|2 | 1/36 [00:02<01:18, 2.25s/it] 44%|####4 | 16/36 [00:02<00:02, 9.03it/s] 61%|######1 | 22/36 [00:02<00:01, 9.95it/s] 72%|#######2 | 26/36 [00:03<00:00, 10.30it/s] 81%|######## | 29/36 [00:03<00:00, 10.61it/s] 89%|########8 | 32/36 [00:03<00:00, 10.87it/s] 94%|#########4| 34/36 [00:03<00:00, 10.99it/s] 100%|##########| 36/36 [00:04<00:00, 11.13it/s] 100%|##########| 36/36 [00:04<00:00, 8.78it/s]

0%| | 0/36 [00:00<?, ?it/s] 33%|###3 | 12/36 [00:00<00:00, 117.65it/s] 67%|######6 | 24/36 [00:00<00:00, 23.25it/s] 83%|########3 | 30/36 [00:01<00:00, 17.87it/s] 94%|#########4| 34/36 [00:01<00:00, 16.17it/s] 100%|##########| 36/36 [00:01<00:00, 18.62it/s]

0%| | 0/36 [00:00<?, ?it/s] 39%|###8 | 14/36 [00:00<00:00, 138.61it/s] 78%|#######7 | 28/36 [00:01<00:00, 20.15it/s] 97%|#########7| 35/36 [00:01<00:00, 16.23it/s] 100%|##########| 36/36 [00:01<00:00, 18.72it/s]

0%| | 0/36 [00:00<?, ?it/s] 39%|###8 | 14/36 [00:00<00:00, 66.99it/s] 58%|#####8 | 21/36 [00:00<00:00, 22.58it/s] 69%|######9 | 25/36 [00:01<00:00, 18.48it/s] 78%|#######7 | 28/36 [00:01<00:00, 16.51it/s] 83%|########3 | 30/36 [00:01<00:00, 15.72it/s] 89%|########8 | 32/36 [00:01<00:00, 14.99it/s] 94%|#########4| 34/36 [00:01<00:00, 14.14it/s] 100%|##########| 36/36 [00:02<00:00, 13.78it/s] 100%|##########| 36/36 [00:02<00:00, 17.69it/s]

0%| | 0/36 [00:00<?, ?it/s] 39%|###8 | 14/36 [00:00<00:00, 100.00it/s] 67%|######6 | 24/36 [00:01<00:00, 20.29it/s] 81%|######## | 29/36 [00:01<00:00, 17.10it/s] 92%|#########1| 33/36 [00:01<00:00, 15.66it/s] 100%|##########| 36/36 [00:02<00:00, 14.97it/s] 100%|##########| 36/36 [00:02<00:00, 18.00it/s]

If you use this tool please cite: https://pubs.rsna.org/doi/10.1148/ryai.230024

Resampling... Resampled in 10.76s Predicting part 1 of 5 ... Predicting part 2 of 5 ... Predicting part 3 of 5 ... Predicting part 4 of 5 ... Predicting part 5 of 5 ... Predicted in 104.88s Resampling... Saving segmentations... Saved in 3.18s Importing segmentation results... Cleaning up temporary folder... Processing completed in 147.69 seconds

Processing finished.

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

lassoan commented 1 year ago

I've found the root cause of the issue and submitted a pull request with the fix (https://github.com/wasserth/TotalSegmentator/pull/202)