The solution that I found for the stride of 2 is:
torch.nn.ConvTranspose3d(
    in_channels=number_of_filters,
    out_channels=number_of_filters,
    kernel_size=kernel_size,
    stride=2,
    padding=kernel_size // 2,
    output_padding=kernel_size % 2,
)

When I have free time I will think of how to do it for strides that are different from 2, but for now, I need to adapt it to non-isotropic kernels.
Thanks a lot Thomas for all the help and pointers!
Stay safe!