Add high-level brain MRI transforms for preprocessing

🚀 Feature

Add some high-level brain MRI transforms for preprocessing.

Motivation

Arguably, there are three preprocessing steps performed on most multimodal neuroimaging studies:

1. Coregistration of the different modalities
2. Brain segmentation/skull-stripping
3. Registration to a reference space, typically MNI

I typically use NiftyReg for registration and ROBEX for brain extraction. As discussed with @ReubenDo, other modern, robust and more Python-friendly tools that could be used for this are SimpleElastix or ANTsPy for registration and HD-BET for brain extraction, similar to what’s done in MRIPreprocessor.

A related transform that might be useful is a defacing transform. The simplest way to do this is using a mask defined in the MNI space, therefore this is very related to the MNI registration.

Pitch

Add new preprocessing transforms, not meant to be used during training. Some ideas: BrainExtraction, ToMNI, Coregister. The requirements would be optional, rising an error with an informative message asking the user to install them using pip.

@romainVala, do you think this would be useful?

[romainVala]

and @GReguig or I will also do a PR for a new motion transform, (with coregistration, among other adds) but still a few things to finish first …

[fepegar]

Looking forward to those papers! TorchIO has received a couple of citations from ARAMIS, but not from the CENIR 😃