pep 8 & pep 257 style improvements and some cleanup

[ofgulban]

Hi again,

• I have linted the whole project (following pep 8 & 257)
• went through the code did some cleanup
• improved status prints.
• did a one liner fix to make it work with both nii and nii.gz data

I did not change anything fundamental and tested the the results with several images. Everything seems to work as it was before so I thought you might like to incorporate this cleanup.

I am actually planning to add a few features that I need to apply defacing to some esoteric 7T data. Once I have implemented those features I will do another PR. However that one will be more intrusive in a way that maybe you would not want to have all those changes.

[chrisgorgo]

Thanks! Looking forward to the 7T contribution - especially curious how you are handling the atypical noise outside the skull.