Jakob Wasserthal
Jakob Wasserthal
This is a known issue and needs to be solved by nnUNet: https://github.com/MIC-DKFZ/nnUNet/issues/2396
This seems like a problem with the 3D Slicer extension. I am not familiar with the details of the extension. Probably the folks in the 3D Slicer forum can help...
Unfortunately I can not reproduce this issue. When I run it it works fine. Can you give more details: Which operating system and which TotalSegmentator version are you using?
There are indeed several cases with errors in the vertebrae ground truth in the training data (the same is true for the ribs). Fixing these kind of errors is very...
If providing TotalSegmentator with more and better data, then the segmentations will improve. But it is not guaranteed by how much they will improve. TotalSegmentator is based on 1.5mm resolution....
No worries! Could you share the IDs of the cases where you found errors? Then I could inspect them.
Probably your weights file got corrupted during download. Can you try to remove the directory `~/.tractseg`? This will delete all the weights and then run again. Then all weights should...
This typically happens when you run into RAM limits. You need more RAM or a smaller image.
Did you have a look into the `lung_vessels` subtask? Does this solve some of your problems?
Thanks for reporting this issue. The server seems to be working. I guess the DICOM was broken in some way. Have you tried with a nifti image?