[ENH]: Add mrdegibbs and dwibiascorrect from mrtrix3 #2904
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| >>> import nipype.interfaces.mrtrix3 as mrt | ||
| >>> unring = mrt.MRDeGibbs() | ||
| >>> unring.inputs.in_file = 'dwi.mif' | ||
| >>> unring.cmdline # doctest: +ELLIPSIS |
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i don't think you need the ELLIPSIS option
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| class DWIDenoiseOutputSpec(TraitedSpec): | ||
| out_file = File(desc="the output denoised DWI image", exists=True) | ||
| out_noisemap = File(desc='the output noise map', exists=True) |
| genfile=True) | ||
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| class DWIBiasCorrectOutputSpec(TraitedSpec): | ||
| out_bias = File(desc='the output estimated bias field') |
| >>> import nipype.interfaces.mrtrix3 as mrt | ||
| >>> bias_correct = mrt.DWIBiasCorrect() | ||
| >>> bias_correct.inputs.in_file = 'dwi.mif' | ||
| >>> bias_correct.cmdline # doctest: +ELLIPSIS |
Codecov Report
@@ Coverage Diff @@
## master #2904 +/- ##
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+ Coverage 67.56% 67.57% +<.01%
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Files 343 343
Lines 43604 43648 +44
Branches 5427 5429 +2
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+ Hits 29461 29493 +32
- Misses 13438 13443 +5
- Partials 705 712 +7
Continue to review full report at Codecov.
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Thanks for your feedback @mgxd! I reverted my variable name change to dwidenoise in case it affects existing code using it. Also modified the arguments to the optional output files. |
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tests should start passing again if you merge with master |
| @@ -28,16 +28,17 @@ class DWIDenoiseInputSpec(MRTrix3BaseInputSpec): | |||
| desc='set the window size of the denoising filter. (default = 5,5,5)') | |||
| noise = File( | |||
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it doesn't look like this is currently being tracked as an output by the interface, but if this is set it I think dwidenoise would make it. You should :
- re-add it to the OutputSpec (
noise = File(..., exists=True) - add a
_list_outputs()method that checks ifself.inputs.noiseis defined, and if so adds it to outputs.
Here's an example of (2) - though you won't have to generate a filename.
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@mgxd I finished incorporating your suggestions. Let me know if there's anything else I'm missing. |
Summary
Addition of dwibiascorrect references #1126
List of changes proposed in this PR (pull-request)
Acknowledgment
I acknowledge that this contribution will be available under the Apache 2 license.