Add a --fs-reuse-base option to reuse existing freesurfer outputs from a longitudinal pipeline

[bpinsard]

Changes proposed in this pull request

Integrate options/configs for nipreps/smriprep#371

Documentation that should be reviewed

[effigies]

I hate to do this to you, but we're going to be merging in the next branches to smriprep and fmriprep pretty soon. I'm afraid you have some rebasing in front of you.

[bpinsard]

Lol thanks for the heads-up, no problem. I will start to update myself on the next changes. Is there an overview/working document that I could start reading from? Thanks!

[effigies]

We don't exactly have a single roadmap we're updating. Issues have been opened, closed and duplicated. I've tried to track them with the next label. (And on smriprep.)

The basic idea is that we're refactoring into a minimal "fit" workflow and an optional apply workflow. The goal is to spend archive space on the things that are expensive to compute and leave the deterministic derivatives to the end user if they want them. (We're working on wiring those up by default now.)

Probably the best place for you to start is here:

https://github.com/nipreps/smriprep/blob/next/smriprep/workflows/anatomical.py#L949-L1001

That's the bit for FreeSurfer, and gives a sense of the overall architecture: Check for pre-computed derivatives, build out workflow if they aren't found, and save them to the output directory. buffer nodes are used as checkpoints that we either populate from precomputed derivatives or subworkflows.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (978ae51) 46.89% compared to head (9dc0a6b) 46.93%.

Additional details and impacted files

@@            Coverage Diff             @@
##             next    #3105      +/-   ##
==========================================
+ Coverage   46.89%   46.93%   +0.03%     
==========================================
  Files          53       53              
  Lines        4224     4227       +3     
==========================================
+ Hits         1981     1984       +3     
  Misses       2243     2243              

Files	Coverage Δ
fmriprep/cli/parser.py	82.89% <100.00%> (+0.07%)	⬆️
fmriprep/config.py	81.79% <100.00%> (+0.08%)	⬆️
fmriprep/workflows/base.py	16.86% <ø> (ø)

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[bpinsard]

Tests should pass when nipreps/smriprep#371 will be merged into smriprep next.