FIX: Remove nonfunctional ANTs registration flag #999
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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.
Should fix the test suite.
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could this be merged or rebased on the current master and the auto tests updated with also add a line to the CHANGES file. |
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Merged current master, ran Suite passes on my machine now. I'll make a new PR for the other changed flags in #1014. |
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I didn't include the |
| collapse_linear_transforms_to_fixed_image_header = traits.Bool( | ||
| argstr='%s', default=False, usedefault=True, desc='') | ||
| # collapse_linear_transforms_to_fixed_image_header = traits.Bool( | ||
| # argstr='%s', default=False, usedefault=True, desc='') |
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these two lines should be deleted.
FIX: Remove extraneous comments
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FIX: Remove nonfunctional ANTs registration flag
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As of 25 days ago, ANTs now has a "command line robustness" feature (introduced in their PR no. 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 but is still passed by the nipype interface. Until the robustness feature was introduced, it was just silently ignored.However, now with a fresh-from-source ANTs build, all nipype.interface.ants.Registration operations fail with the message:
There is no provision to turn this flag off completely; the interface always passes something so Ants always throws a fit. Until this flag actually works again on ANTs' end, we should disable the flag in the registration interface.
Since it may be reintroduced I opted to comment it out rather than delete the lines.