Comments (2)
mattcieslak
commented on August 14, 2024
1
Ok this is really good to know. If sdcflows revisits topup we should be careful about orientations when making the 4D inputs
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oesteban
commented on August 14, 2024
I know FSL uses voxel coordinates for a lot of its algorithms
I guess the only problematic case here would be FUGUE, and I think it would choke when passed a fieldmap with different matrix size.
However, in SDCflows we stopped using FUGUE and things are done in physical coordinates space. This means that you can keep the accuracy of your fieldmap (it is not going to give you substantially better results, except for edge cases where a spike is present and it makes it to the final, resampled map).
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Related Issues (20)
- Generate untransformed fieldmap in reference space
- Support BIDS-URIs in `IntendedFor`
- Tracking LAS phasediff issue HOT 3
- Add --bids-filter-file to sdcflows-find-estimators
- *The problem* of SDCFlows (and how to fix it) HOT 11
- Slightly rotated phase1/phase2 images should not fail to be aligned HOT 9
- Partial fieldmaps still failing (phasediff w/o magnitude)
- syn preprocessing `epi_reference_wf` does not distinguish between different matrix sizes HOT 6
- Distortion correction translating instead of unwarping HOT 5
- Verify SyN can be constructed with B0FieldIdentifier HOT 1
- Poor SyN registration HOT 2
- SyN-SDC includes multiple echos
- Ridge regression in BSplineApprox can randomly produce garbage HOT 2
- Revise tolerance of ``sdcflows/interfaces/tests/test_bspline.py::test_bsplines``
- ``scipy.signal.cubic`` is now deprecated HOT 3
- `HCP101006/sub-101006/fmap/sub-101006_dir-LR_epi.json` has wrong sign in PE direction HOT 8
- Unable to `pkg_resources.resource_filename` to locate data files HOT 1
- Implement Jacobian attenuation in the target space
- Add function to selectively remove estimators from the registry
- Wrangler: discard `part-phase` from `_epi` HOT 1
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