feat(syn): Update totalFieldVarianceInVoxel space based on voxel resolution #487
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## master #487 +/- ##
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+ Coverage 83.98% 84.32% +0.34%
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I've been reading ANTsX/ANTs#734, and it looks all measurements are relative to the fixed image, so I should change this from moving to fixed. |
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effigies
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Mar 26, 2025
oesteban
previously approved these changes
Mar 26, 2025
| syn_config = data.load(f"sd_syn{'_sloppy' * sloppy}.json") | ||
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| vox_params = pe.Node(niu.Function(function=_mm2vox), name="vox_params") | ||
| vox_params.inputs.registration_config = json.loads(syn_config.read_text()) |
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Since we need to read the config outside the Registration node, we might want to extract the number of levels from it (e.g., len(config_dict['transforms']) instead of hard-code the magic number (of 2). It will be a bit trickier for handling masks, but a bit more robust, IMHO.
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But probably for another PR btw
Co-authored-by: Oscar Esteban <[email protected]>
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2.13.0 (May 15, 2025) Feature release in the 2.13.x series. This release addresses some longstanding issues with the SyN-SDC workflow, improving the registration quality in adult humans by utilizing a spatial prior, as well as allowing Laplacians to be up- or down-weighted in the cost function, making it more usable across species. Additionally, this release allows for the use of ``EstimatedTotalReadoutTime`` or ``EstimatedEchoSpacing``, or a manually provided fallback ``TotalReadoutTime`` value, permitting the use of SDCFlows on datasets that do not have reliable timing information without introducing incorrect metadata into the datasets. * fix(syn): Re-enable priors respecting ``sd_priors`` argument (#488) * feat: Add workflow arguments for metadata estimates and fallback TRT (#479) * feat(syn): Update totalFieldVarianceInVoxel space based on voxel resolution (#487) * feat(syn): Allow changing laplacians weights in SyN registration metric (#484) * test(syn): Add a test to exercise SyN workflow creation and check parameters (#486)
effigies
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May 15, 2025
2.13.0 (May 15, 2025) Feature release in the 2.13.x series. This release addresses some longstanding issues with the SyN-SDC workflow, improving the registration quality in adult humans by utilizing a spatial prior, as well as allowing Laplacians to be up- or down-weighted in the cost function, making it more usable across species. Additionally, this release allows for the use of ``EstimatedTotalReadoutTime`` or ``EstimatedEchoSpacing``, or a manually provided fallback ``TotalReadoutTime`` value, permitting the use of SDCFlows on datasets that do not have reliable timing information without introducing incorrect metadata into the datasets. * fix(syn): Re-enable priors respecting ``sd_priors`` argument (#488) * feat: Add workflow arguments for metadata estimates and fallback TRT (#479) * feat(syn): Update totalFieldVarianceInVoxel space based on voxel resolution (#487) * feat(syn): Allow changing laplacians weights in SyN registration metric (#484) * test(syn): Add a test to exercise SyN workflow creation and check parameters (#486)
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The SyN transform parameters are:
The size of estimated displacements should not depend significantly on the voxel size. This change updates the totalFieldVarianceInVoxelSpace to mm values of 10mm and 0.5mm in the
sd_syn.jsonfiles, and adds an interface to convert these to voxels based on the resolution in the phase-encoding direction.