Add bug fixes from red branch
#161
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- Both for volume and surface files - Does not terminate for surface files, needs to be fixed - Also refactor smoothing to use AFNI's `3dBlurToFWHM`
- When `run_reconall` is enabled
- PyBIDS will automatically remove them, because they do not conform to the spec - For now, we simply rename these tags to `acq`
- This should make it easier to diagnose when field maps are incompatible or not correctly converted to BIDS format
- During BIDS conversion - Make correct relative path
- Also create a `Factory` to reduce duplicate computation - We will also need the outputs for the `bold_grayords_wf`
HippocampusGirl
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Codecov Report
@@ Coverage Diff @@
## main #161 +/- ##
==========================================
+ Coverage 52.59% 53.44% +0.84%
==========================================
Files 209 211 +2
Lines 11406 11472 +66
Branches 1948 1960 +12
==========================================
+ Hits 5999 6131 +132
+ Misses 5012 4920 -92
- Partials 395 421 +26
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