N4BiasFieldCorrection fails for compiled ANTS #3138
Description
Summary
N4BiasFieldCorrection throws an error
Actual behavior
The rescale_intensities trait is set by default to False while it must not be specified for ANTS version under 2.1.0
Expected behavior
rescale_intensities should be undefined by default
How to replicate the behavior
We can replicate the behavior with compiled ANTs
Script/Workflow details
My Ants version
salma@salma-Latitude-E7450:~/CODE/sammba-mri $ N4BiasFieldCorrection --version ANTs Version: 0.0.0.0 Compiled: Dec 22 2019 22:03:46Ants version as read by nipype
salma@salma-Latitude-E7450:~/CODE/sammba-mri $ python -c "from nipype.interfaces import ants; print(ants.base.Info.version())" 200104-19:14:53,203 nipype.utils INFO: Running nipype version 1.5.0-dev+g7f6cc2de2 (latest: 1.4.0) 0.0.0from nipype.interfaces import ants bias_correct = ants.N4BiasFieldCorrection().run bias_correct(input_image='/tmp/func.nii.gz')throws the following error
200104-19:20:52,963 nipype.utils INFO: Running nipype version 1.5.0-dev+g7f6cc2de2 (latest: 1.4.0) --------------------------------------------------------------------------- Exception Traceback (most recent call last) <ipython-input-1-9321c82e17d6> in <module> 2 3 bias_correct = ants.N4BiasFieldCorrection().run ----> 4 bias_correct(input_image='/tmp/func.nii.gz') ~/CODE/nipype/nipype/interfaces/base/core.py in run(self, cwd, ignore_exception, **inputs) 348 self.inputs.trait_set(**inputs) 349 self._check_mandatory_inputs() --> 350 self._check_version_requirements(self.inputs) 351 interface = self.__class__ 352 self._duecredit_cite() ~/CODE/nipype/nipype/interfaces/base/core.py in _check_version_requirements(self, trait_object, raise_exception) 281 raise Exception( 282 "Trait %s (%s) (version %s < required %s)" --> 283 % (name, self.__class__.__name__, version, min_ver) 284 ) 285 Exception: Trait rescale_intensities (N4BiasFieldCorrection) (version 0.0.0 < required 2.1.0) while forcing the trait rescale_intensities to be undefined solves the issue
from nipype.interfaces.base import traits bias_correct(input_image='/tmp/func.nii.gz', rescale_intensities=traits.Undefined)Platform details:
200104-19:19:19,39 nipype.utils INFO: Running nipype version 1.5.0-dev+g7f6cc2de2 (latest: 1.4.0) {'commit_hash': '7f6cc2de2', 'commit_source': 'repository', 'networkx_version': '2.4', 'nibabel_version': '3.0.0', 'nipype_version': '1.5.0-dev+g7f6cc2de2', 'numpy_version': '1.17.4', 'pkg_path': '/home/salma/CODE/nipype/nipype', 'scipy_version': '1.3.2', 'sys_executable': '/home/salma/miniconda3/bin/python', 'sys_platform': 'linux', 'sys_version': '3.7.4 (default, Aug 13 2019, 20:35:49) \n[GCC 7.3.0]', 'traits_version': '5.2.0'}``` ### Execution environment - My python environment outside container