Here is how to perform the inference for the different folds of Fully automatic segmentation of diffuse large B cell lymphoma lesions on 3D FDG-PET/CT for total metabolic tumour volume prediction using a convolutional neural network..
You will first need and assure that the nnunet library is correctly working and configure required paths.
Weights can be downloaded at the following link
In the PATH_FOLDER every patients should be numbered as patientID_0000 for CT and patientID_0001 for PET in the nifti format wheree CT should be in hounsfield unit and PET in SUV.
Then from the terminal type:
nnUNet_predict -i PATH_FOLDER -o ./PATH_OUTPUT -t 1