Jakob Wasserthal

icon company University Hospital Basel, Research Department icon location Basel

Results 222 comments of Jakob Wasserthal

Future Work on MRI Support?

Extending TotalSegmentator to MRI is on our agenda, but it will be more in the future. This will take at least another year.

sslVerify error when running TS v2

v1 was downloading the weights from zenodo which was slow. v2 is now downloading the weights from github. Not sure why this is blocked by your hospital IT.

sslVerify error when running TS v2

The weights are only downloaded once. But if your download failed, then it does not find any weights on the next run and tries to download them again.

Invalid(?) RTstructs generated

Thanks for mentioning this. TotalSegmentator depends on rt-utils for generating RTstructs. It does not make sense to implement my own logic around that. So I have to wait for them...

Error trying to set the device to GPU in Jupyter notebook

Which totalsegmentator version are you using? Can you update to the newest version?

Error trying to set the device to GPU in Jupyter notebook

Using gpu:1 is only possible in the newest master. In the latest pip version only `--device gpu` is possible.

Number of classes in Python API

When you install the newest pip package the python api will also use the new version. So I guess you still have the old totalsegmentator installted.

Is the Liver Vessel Segmentation function only available in v1? Or did I overlook this feature in v2

Correct, the liver vessel segmentation is not yet available in v2.

Is the Liver Vessel Segmentation function only available in v1? Or did I overlook this feature in v2

Calling the remaining commented code does not work. It is deactivated for a good reason ;). I first have to train a nnunet v2 on the liver vessel data. This...

Why is there only one label for the `vertebral body model`? Can we divide it into different corresponding levels with different labels?

The vertebrae_body mask is intended to be used to refine the individual vertebrae masks. Just take the intersection of both for each vertebrae. Then you have what you need.