Rule updates

[kaitj]

Proposed changes

This PR pulls in and resolves conflicts from #17, #20, and #21. It also resolves previous review comments. Most of these include quality changes. Briefly (click drop toggle to see notes from previous PRs for respective workflows):

Freesurfer

• Update to the thalamic segmentation output file name (which is defined by Freesurfer)
• Uses wildcards to define some of the outputs
• Addition of relevant references in the .smk file

Mrtpipelines

• Updates to pybids_inputs
• Use of variables instead of grabbing from config for every rule
• Renamed rules to reflect similar naming of mrtrix functions
• Update mrtrix container to 3.0.3.

zona_bb_subcortex

• Defines the zona output directory
• Changes for snakefmt
• Fix name of files in resources for zona
• Added anticipated path for anat segmentation for transformation purposes between different MNI spaces and subject native space
  1. These files are available locally at the moment, but are too big to be added to the git repo
• Add transformation to rule to define an transform matrix

All rules have also been updated to make use of functools.partial.

An additional note - a couple of files needed for transformation is too large to be shared via this repository and after a brief discussion, look into downloading it as part of the container build / point users to download location. Need to discuss with @jclauneuro to see what best option is here (files are SNSX32 related, namely T1w and subcortical segmentations in MNI152NLin6Asym and MNI152Nlin2009b space)

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 functionalitiy)
• 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.

[kaitj]

Syntaxes and workflow bugs have been fixed as of c5b4856. Also did a dry-run through the workflow to ensure it works (although labelmerge not added yet).

[tkkuehn]

A couple of generally minor changes but I think this is very close to being ready to merge

[tkkuehn]

One nitpick and one small change

[kaitj]

@tkkuehn Above changes should be fixed. I also found a few other workflow piping issues (namely incorrect use of wildcards in certain rules) that need to be corrected for when I was adding in resources and logs. Will throw that in a separate PR.

[tkkuehn]

One tiny comment but this is otherwise good to merge, so I don't need to review it again after