Customize SegmentationUNet.py

[stka85]

Hi, I am trying to run Live US Segmentation in Slicer and have customized the loading and preprocessing of the input/output image to my training net. However, the SegmentationUNet extension is no longer visible in the Slicer modules. I am using a FlexibleUNet and Pytorch (Monai Template). How can I adapt the SegmentationUNet.py so that it is available in Slicer?

[ungi]

Hi, we don't usually install Pytorch (or TensorFlow) in Slicer's python anymore, so there is no extension that would run an AI model in Slicer. Instead, implement a small python program that communicates with Slicer via OpenIGTLink. Here is a small example: https://github.com/SlicerIGT/aigt/blob/master/UltrasoundSegmentation/Inference/ScanConversionInference.py

I think there is a more complex example here: https://github.com/SlicerIGT/aigt/tree/master/DeepLearnLive/RunNeuralNet
This second example is a Slicer module that may start the external program for you.