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Update registration.py
As of 25 days ago, ANTs now has a "command line robustness" feature (see their PR no.126: ANTsX/ANTs#126) which forces all provided options to actually mean/do something. This particular option, `--collapse-linear-transforms-to-fixed-image-header`, has been [nonfunctional since December 2012](https://github.com/stnava/ANTs/blame/3b906d86a1b455714983083989417003425cd43c/Examples/antsRegistration.cxx#L76) but is still passed by the nipype interface. As a result, with a fresh-from-source ANTs build, all nipype.interface.ants.Registration calls now fail with the message: ``` Standard output: ERROR: Invalid flag provided collapse-linear-transforms-to-fixed-image-header Standard error: ERROR: Invalid command line flags found! Aborting execution. Return code: 1 ``` There is no provision to turn off this flag; the interface always passes the default of 0 (False). Until this flag actually works again on ANTs' end, we should disable the flag in the registration interface.
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nipype/interfaces/ants/registration.py

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@@ -320,8 +320,8 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
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low=0.0, high=1.0, value=1.0, argstr='%s', usedefault=True, desc="The Upper quantile to clip image ranges")
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winsorize_lower_quantile = traits.Range(
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low=0.0, high=1.0, value=0.0, argstr='%s', usedefault=True, desc="The Lower quantile to clip image ranges")
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collapse_linear_transforms_to_fixed_image_header = traits.Bool(
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argstr='%s', default=False, usedefault=True, desc='')
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# collapse_linear_transforms_to_fixed_image_header = traits.Bool(
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# argstr='%s', default=False, usedefault=True, desc='')
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class RegistrationOutputSpec(TraitedSpec):

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