Replace fslmaths with python scripts

[kaitj]

Proposed changes

Resolves #64. Uses nibabel instead of fslmaths to perform necessary mathematical operations to create masks.
I thought about combining the two rules that called fslmaths, but ultimately decided against it (for now) to keep it simple for handling the --skip_brainstem option.

Types of changes

What types of changes does your code introduce? Put an x in the boxes that apply

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Other (if none of the other choices apply)

Checklist

Put an x in the boxes that apply. You can also fill these out after creating the PR. If you are unsure about any of the choices, don't hesitate to ask!

• Changes have been tested to ensure that fix is effective or that a feature works.
• Changes pass the unit tests
• Code has been run through the poe quality task
• I have included necessary documentation or comments (as necessary)
• Any dependent changes have been merged and published

Notes

All PRs will undergo the unit testing before being reviewed. You may be requested to explain or make additional changes before the PR is accepted.

[tkkuehn]

Looks good to me assuming you've given the scripts a try

[kaitj]

Yep, tested this and it appears to be working. Will merge this in too.