Labelmerge

[kaitj]

Proposed changes

Update (Nov 30): Changed the base branch to dry-run as the tests were helpful to making sure that the changes don't break the workflow.

• Updates zona_bb_subcortex.smk with rule for labelmerge
  • Adds container for labelmerge within the params, so that singularity run can be called. Otherwise snakemake just tries to run the rule using the container as a dependency.
• Also adds / updates resource files necessary for workflow to run
  • Note, only MNI152NLin6Asym T1w template from templateflow is added. Can easily go between the 2 commonly used MNI spaces and this is sufficient for getting a transformation to subject space. In the future, we can look at requiring fmriprep / adding an fmriprep as suggested during the weekly meeting.

One note is that this PR assumes that khanlab/labelmerge#22 is good to proceed.

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.

[tkkuehn]

Looks good, just wanna make sure the double check comment isn't blocking before I merge this.

[tkkuehn]

What are we double checking here?

[kaitj]

Ahh, this was a note to my self, I removed it in one of the other PRs. Just wanted to check the conditional was written correctly by comparing with an existing rule written in another workflow.

[tkkuehn]

Tests are failing because the labelmerge branch doesn't have the test data. I'll merge this and make sure the tests complete on the dry-run branch.