Add round() when loading NIfTI for atlas building#14
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Simple update to round data when loading in a NIfTI volume, in the case where segment indices are stored as floats rather than ints per voxel (could either be in raw data itself or introduced as part of interpolation)
…tlas This commit adds a test script to specifically check subcortical atlas building functionality that uses the proposed round() addition to account for float imprecision during conversion
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Hi @teanijarv and collaborators, thank you for sharing this amazing package! So useful and exceptionally well-documented, with a straightforward user interface and high-quality renderings 😊
While noodling around with the
build_subcortical_atlasfunction across a variety of subcortical atlases, I found that no meshes were created for one atlas. Upon inspection, at least when loaded withnibabel, the voxel index values were floats instead of integers (e.g., 2.99999 when the index should just be 3). I believe this arises from issues with float format and precision.As a proposed fix for that case (which other volumes may also encounter), I've added a
.round()function call when loading in the NIfTI volume inbuild_subcortical_atlas. This change is in line 292 ofatlas_builder.py. I also added a new testing scripttests/test_atlas_builder.pyand confirmed all tests passed withuvon my end.Hope this is helpful, and I'm very happy to tweak if needed.
Cheers,
Annie 😊