mrtpipelines.smk

[kaitj]

Reorganize this part of the workflow. Can be broken down into 3 separate phases (groups):

Breakdown:

participant1 (phase1):

• Perform processing up to computing average response function

group (phase2):

• Compute average response function

participant2 (phase3):

• Processing (including tractography) using the average response function

Most of the notes within the code that has TODO would be nice to have for a v0.2.x

TODO:

• [x] Check for any needed updates for new snakebids version
• [x] Add group directive to rules
• [ ] Fix the loop to update and extract individual connections
  • [ ] Optionally save 3D (.tck) files of connections

Can look at preproc pipeline used for @mtayl84's workflow.