liver_vessels subtask invokes model download everytime

[ASHISRAVINDRAN]

Hi @wasserth
I am from the MITK development team working to update TotalSegmentator to v2.4 for our upcoming release.
I am testing out inferencing all subtasks as part of sanity test. I see that subtask liver_vessels invokes model download from internet on every run. Its weights are not ultimately saved in the .totalsegmentator folder found in the $HOME directory after the first run.
It would be great if you can check this.

Thanks in advance

[wasserth]

Unfortunately I can not reproduce this issue. For me the weights are properly stored in the default directory ~/.totalsegmentator/nnunet/results. Which operating system are you using?

[ASHISRAVINDRAN]

I can reproduce on Windows 10 and Ubuntu 22.04.
When I run Totalsegmentator -i .\example_ct.nii.gz -o .\outDir\ -ta liver_vessels I can see a tmp_download_file.zip file in the ~/.totalsegmentator/nnunet/results folder. After inferencing, its gone. Its not persisted or renamed to something in the lines of "DatasetXXX_subtask_partX..."

[mingtian126]

@wasserth Hi, I have some issue when do liver_vessels as well. When I run the following: output_img=totalsegmentator(input_img,preview=False,roi_subset=tasks), where tasks=["liver_vessels"], it gave me the following error:
File "/home/anaconda3/lib/python3.11/site-packages/totalsegmentator/python_api.py", line 358, in totalsegmentator
crop_mask[organ_seg_data == class_map_inv[roi]] = 1
~~~~~~~~~~~~~^^^^^
KeyError: 'liver_vessels'

Please help, Thank you!

[MeirBenin]

Hi @wasserth it seems like it expect for path Task008_HepaticVessel but after the extracting the zip it saved as Dataset008_HepaticVessel