Update inference file for multisequence models

lassoan / SlicerMONAIAuto3DSeg

Extension for 3D Slicer for running MONAI Auto3DSeg models

MIT License

66 stars 10 forks source link

Update inference file for multisequence models #29

Closed diazandr3s closed 8 months ago

diazandr3s commented 8 months ago

Update inference script for multisequence models

This assumes the sequences are coregistered
The keys in the input dictionary image_file are image1, image2, etc

lassoan commented 8 months ago

I added GUI and a dummy model description with two input volumes.

I could not pass a dictionary via command-line on Windows (despite putting the dictionary argument value in single quotes and escaping the double-quotes, fire interpreted the argument as invalid or a string). So I just added a few more simple arguments.

diazandr3s commented 8 months ago

Superb! I've just added the prostate model that works on T2 and ADC MR images.

For this, the user has to load in Slicer the sequences T2 and ADC in separate files.

Source dataset (Task05_Prostate): https://drive.google.com/drive/folders/1HqEgzS8BV2c7xYNrZdEAnrHk7osJJ--2

lassoan commented 8 months ago

Everything seems functional now (except that multiple input images may need to be resampled to the same geometry, but that issue is tracked in https://github.com/lassoan/SlicerMONAIAuto3DSeg/issues/31).