Modify preprocessing script

[sandrinebedard]

Description

This PR modifies the preprocessing to:

• Add CSA computation of soft and hard GT
• Create disc labels, crop and add them to data_processed_clean
• Check if there are NaN values in generated softseg
• Thresholding softsegs between 0 and 1

An example of results can be found under duke/projects/contrast-agnostic-seg/contrast-agnostic-test-2022-08-09-all

[sandrinebedard]

I think this is ready to merge, since the naming convention of MTS will not be addressed here (a least yet)