ENH: Massage TOPUP's fieldcoeff files to be compatible with ours #154
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TOUP-generated "fieldcoeff" files are just B-Spline fields, where the shape of the field is fixated to be a decimated grid of the original image by a factor of 2x and added 3 pixels on each dimension. This is one root reason why TOPUP errors (FSL 6) or segfaults (FSL5), when the input image has odd number of voxels along one or more directions. These "fieldcoeff" are fixated to be zero-centered, and have "plumb" orientation (as in, aligned with cardinal/imaging axes). The q-form of these NIfTI files is always diagonal, with the decimation factors set on the diagonal (and hence, the voxel zooms). The origin of the q-form is set to the reference image's shape. This interface modifies these coefficient files to be fully-fledged NIfTI images aligned with the reference image. Therefore, the s-form header of the coefficients file is updated to match that of the reference file. The s-form header is used because the imaging axes may be oblique. The q-form retains the original header and is marked with code 0.
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Codecov Report
@@ Coverage Diff @@
## master #154 +/- ##
==========================================
- Coverage 94.62% 94.44% -0.18%
==========================================
Files 19 19
Lines 1135 1171 +36
Branches 150 153 +3
==========================================
+ Hits 1074 1106 +32
- Misses 34 37 +3
- Partials 27 28 +1
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2.0.0rc4 * FIX: Convert SEI fieldmaps given in rad/s into Hz (#127) * FIX: Limit ``3dQwarp`` to maximum 4 CPUs for stability reasons (#128) * ENH: Generate a simple mask after correction (#161) * ENH: Increase unit-tests coverage of ``sdcflows.fieldmaps`` (#159) * ENH: Optimize tensor-product B-Spline kernel evaluation (#157) * ENH: Add a memory check to dynamically limit interpolation blocksize (#156) * ENH: Massage TOPUP's fieldcoeff files to be compatible with ours (#154) * ENH: Add a simplistic EPI masking algorithm (#152) * ENH: Utility that returns the ``B0FieldSource`` of a given potential EPI target (#151) * ENH: Write ``fmapid-`` entity in Derivatives (#150) * ENH: Multiplex fieldmap estimation outputs into a single ``outputnode`` (#149) * ENH: Putting the new API together on a base workflow (#143) * ENH: Autogenerate ``B0FieldIdentifiers`` from ``IntendedFor`` (#142) * ENH: Finalizing the API overhaul (#132) * ENH: Keep a registry of already-used identifiers (and auto-generate new) (#130) * ENH: New objects for better representation of fieldmap estimation (#114) * ENH: Show FieldmapReportlet oriented aligned with cardinal axes (#120) * ENH: New estimation API (featuring a TOPUP implementation!) (#115) * DOC: Minor improvements to the literate workflows descriptions. (#162) * DOC: Fix typo in docstring (#155) * DOC: Enable NiPype's sphinx-extension to better render Interfaces (#131) * MAINT: Drop Python 3.6 (#160) * MAINT: Enable Git-archive protocol with setuptools-scm-archive (#153) * MAINT: Migrate TravisCI -> GH Actions (completion) (#138) * MAINT: Migrate TravisCI -> GH Actions (#137) * MAINT: Minimal unit test and refactor of pepolar workflow node (#133) * MAINT: Collect code coverage from tests on Circle (#122) * MAINT: Test minimum dependencies with TravisCI (#96) * MAINT: Add FLIRT config files to prepare for TOPUP integration (#116)
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TOPUP-generated "fieldcoeff" files are just B-Spline fields, where the shape
of the field is fixated to be a decimated grid of the original image by a
factor of 2x and added 3 pixels on each dimension.
This is one root reason why TOPUP errors (FSL 6) or segfaults (FSL5), when the
input image has odd number of voxels along one or more directions.
These "fieldcoeff" are fixated to be zero-centered, and have "plumb" orientation
(as in, aligned with cardinal/imaging axes).
Voxel sizes are always 2.0 (dimensionless).
This interface modifies these coefficient files to be fully-fledged NIfTI images
aligned with the reference image.
Therefore, the s-form header of the coefficients file is updated to match that
of the reference file.
The s-form header is used because the imaging axes may be oblique.
The q-form retains the original header and is marked with code 0.