I have a dataset with MRI of patients with a specific disease that affects the brain and another dataset with MRI of healthy patients.
I want to create a classifier (using neural networks) to classify if the MRI of a new patient shows the presence of the illness or not.
First of all, I extracted the brain from all the MRIs (the so-called skull stripping) using BET tool found in FSL.
I have three questions for you
As the input to the training phase, I want to give the whole extracted brains (possibly in the nii format). What kind of preprocessing steps do I need to apply once I've extracted the brains (before passing it to the classifier)?
Do you know any better tool for skull stripping?
Do you know a tool (or library) that takes as input a nii files and allows me to create a classifier that uses neural networks?