[ENH] Add afni.LocalStat and afni.ReHo, update afni.ROIStats inputs #2740
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## master #2740 +/- ##
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- Coverage 67.42% 64.09% -3.34%
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Files 340 338 -2
Lines 43172 43187 +15
Branches 5353 5359 +6
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- Hits 29110 27679 -1431
- Misses 13363 14439 +1076
- Partials 699 1069 +370
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| mandatory=True, | ||
| exists=True) | ||
| mask = File(desc='input mask', argstr='-mask %s', position=3, exists=True) | ||
| mask_file = File(desc='input mask', argstr='-mask %s', exists=True) |
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When renaming a field, you should use deprecated and new_name (see the developer guide) fields (in addition to the new trait).
mask = File(desc='input mask', argstr='-mask %s', position=3, exists=True,
deprecated='1.1.4', new_name='mask_file')
mask_file = File(desc='input mask', argstr='-mask %s', exists=True)
nipype/interfaces/afni/preprocess.py
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| 'zeromedian': '-median', | ||
| 'zerosigma': '-sigma', | ||
| 'zeromode': '-mode' | ||
| } |
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We (try to) conform to PEP8. Can you restyle this as follows (4 space indentation, no double spaces, closing brace matching entries)?
_stat_dict = {
'mean': '-nzmean',
...
}
nipype/interfaces/afni/utils.py
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| chi_sq = traits.Bool( | ||
| argstr='-chi_sq', | ||
| desc='Output the Friedman chi-squared value in addition to the ' | ||
| 'Kendall\'s W.') |
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Should there be an output that's defined when this is True?
nipype/interfaces/afni/utils.py
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| argstr='-chi_sq', | ||
| desc='Output the Friedman chi-squared value in addition to the ' | ||
| 'Kendall\'s W.') | ||
| mask = traits.File( |
nipype/interfaces/afni/utils.py
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| 'faces': 7, | ||
| 'edges': 19, | ||
| 'vertices': 27, | ||
| } |
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Please reformat this dictionary as above.
nipype/interfaces/afni/utils.py
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| output_spec = ReHoOutputSpec | ||
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| def _list_outputs(self): | ||
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@rciric Could you update the deprecation to 1.1.4? We can't release until the circle builds are resolved, so might as well get this one in. |
effigies
changed the title
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Thanks! |
Summary
3dLocalstatadds support for voxelwise (local) confounds, for use in ANATICOR-like denoising protocols.3dReHoenables estimation of voxelwise and ROI-wise regional homogeneity.3dROIstatshas been reworked to support a broader range of parameters and regional statistics.List of changes proposed in this PR (pull-request)
Localstatinterface added for AFNI's3dLocalstat.ReHointerface added for AFNI's3dReHo.ROIstatsinput spec accepts new parameters:num_roi,zerofill,roisel,debug,nomeanout,nobriklab,format1D,format1DR, andstat. This means that parameters to theROIstatsinterface can now be used to specify computation of regional statistics other than the default zero-inclusive mean.ROIstatsare not backward-compatible; for instance, the output has been renamed fromstatstoout_file. Software using the existingROIstatsinterface will need to be updated accordingly.Questions
ROIstatscurrently favour internal consistency, but it would be no trouble to change theROIstatsinterface to be fully backward-compatible instead.Acknowledgment