Add ANTs' KellyKapowski interface #1845
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this is something related with the output of the example. maybe I have to add the 'u' in the beginning of the output string? thanks! |
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| def _list_outputs(self): | ||
| outputs = self._outputs().get() | ||
| outputs['cortical_thickness'] = os.path.abspath(self._gen_filename('cortical_thickness')) |
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could we use namesource and template for these two?
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do you mean to change the name of the output parameters?
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e.g., like this
nipype/nipype/interfaces/freesurfer/preprocess.py
Line 1506 in 0620aba
then you can get rid of the list_outputs function.
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done. thanks for the review. |
| desc="Maximum number of iterations for estimating the invert \n" | ||
| "displacement field.") | ||
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| cortical_thickness = File(argstr='--output "%s"', genfile=True, keep_extension=True, |
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i don't think genfile is required here.
| skip += ['warped_white_matter', 'gray_matter_label', 'white_matter_label'] | ||
| return super(KellyKapowski, self)._parse_inputs(skip=skip) | ||
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| def _gen_filename(self, name): |
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i think you can delete this function as well.
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If I delete this function, how do I format the output parameter for the commandline in the _format_arg function?
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I had to do this because the output command argument is a 2-file argument with the values of cortical_thickness and warped_white_matter:
--output "[segmentation0_cortical_thickness.nii.gz,segmentation0_warped_white_matter.nii.gz]"
Is there a better way to do this? This is the scheme I could find in other ANTs interfaces.
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@alexsavio - could you please merge with master and push - we have been trying to clean up travis/circle tests. |
Hi,
This is the command for DiReCT cortical thickness measuring. Instead of using the whole antsCorticalThickness.sh script (which includes bias-field correction, warping, tissue segmentation, etc..).
This study shows that other combinations using only DiReCT can lead to more robust results:
http://dx.doi.org/10.1016/j.nicl.2016.05.017