I started working on the application of deep learning in medical imaging recently. While dealing with MRI images in the BraTS dataset, I observe that first and last few frames are always completely empty (black). I want to ask those who are already working in the field, is there a way to remove them in a procedural manner before training and add them correctly after the training as a postprocessing step (to comply with the ground truth segmentations' shape)? Has anyone tried that? I could not find any results on Google. So asking here.
Edit: I think I did not make my point clear enough. I meant to say first and last few frames of each MRI scan are empty. How to deal with those is what I intended to ask.