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@tsalo tsalo commented Nov 18, 2025

Closes #510. This adds a t2w_preproc query to the io_spec.json and an extra workaround for queries that start with t2w_ in collect_derivatives. I don't think this is the most elegant solution, so I'm happy to switch to another approach if one makes sense.

@tsalo tsalo added the bug Something isn't working label Nov 18, 2025
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codecov bot commented Nov 18, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 74.82%. Comparing base (bf1df32) to head (93cb2ee).

Additional details and impacted files
@@            Coverage Diff             @@
##           master     #512      +/-   ##
==========================================
+ Coverage   70.61%   74.82%   +4.20%     
==========================================
  Files          25       25              
  Lines        2083     2085       +2     
  Branches      272      273       +1     
==========================================
+ Hits         1471     1560      +89     
+ Misses        553      456      -97     
- Partials       59       69      +10     
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Co-authored-by: Chris Markiewicz <effigies@gmail.com>
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tsalo commented Nov 19, 2025

One other idea: what about this

  • Change preproc to preproc_t1w and t2w_preproc to preproc_t2w
  • Change if not key.startswith('t2w_') to if not key.startswith('preproc_')
  • Prepend anat_ instead of t1w_.

I think that's more readable for T2w-focused workflows like Nibabies.

EDIT: After looking through the workflows a bit more, I see that this require a heavy lift to make sure workflow inputs and outputs use consistent names.

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t2w_preproc query not specified in io_spec.json

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