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Why my segmentations don't seem to be saved? #306
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If you see please help me, this is very important to me, thank you sincerely. |
Does the "total" task work? ( |
I'm not sure if it has anything to do with the system, I'm using win11, is the latest version of totalsegmentator a must to use linux? Because I ran into this issue while training nnUNetv2, nnUNetv2 2.3 onwards would get an error. |
I solved this problem! To a large extent it is related to the system, we need linux. |
I followed your tutorial step by step, but the result I got was like the segmentation was not saved。
Here's the statement I typed and the result I got:
You can see that the segmentation is not saved, and I have used the slicer software to see that there is indeed no predicted result, and nothing is displayed.
(d:\totalsegmentotar.conda) D:\totalsegmentotar>TotalSegmentator -i hip_left.nii.gz -o segmentations -ta hip_implant
If you use this tool please cite: https://pubs.rsna.org/doi/10.1148/ryai.230024
No GPU detected. Running on CPU. This can be very slow. The '--fast' or the
--roi_subset
option can help to reduce runtime.Generating rough body segmentation...
Resampling...
Resampled in 1.93s
Predicting...
d:\totalsegmentotar.conda\Lib\site-packages\nnunetv2\utilities\plans_handling\plans_handler.py:37: UserWarning: Detected old nnU-Net plans format. Attempting to reconstruct network architecture parameters. If this fails, rerun nnUNetv2_plan_experiment for your dataset. If you use a custom architecture, please downgrade nnU-Net to the version you implemented this or update your implementation + plans.
warnings.warn("Detected old nnU-Net plans format. Attempting to reconstruct network architecture "
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 1.12it/s]
Predicted in 12.95s
Resampling...
WARNING: Could not crop because no foreground detected
cropping from (333, 333, 539) to (333, 333, 539)
Predicting...
d:\totalsegmentotar.conda\Lib\site-packages\nnunetv2\utilities\plans_handling\plans_handler.py:37: UserWarning: Detected old nnU-Net plans format. Attempting to reconstruct network architecture parameters. If this fails, rerun nnUNetv2_plan_experiment for your dataset. If you use a custom architecture, please downgrade nnU-Net to the version you implemented this or update your implementation + plans.
warnings.warn("Detected old nnU-Net plans format. Attempting to reconstruct network architecture "
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 64/64 [04:27<00:00, 4.18s/it]
Predicted in 288.96s
Saving segmentations...
0%| | 0/1 [00:00<?, ?it/s]Creating hip_implant.nii.gz
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:04<00:00, 4.61s/it]
Saved in 6.80s
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