[ENH] Add afni.LocalStat and afni.ReHo, update afni.ROIStats inputs #2740

rciric · 2018-10-20T03:13:24Z

Summary

A new interface for 3dLocalstat adds support for voxelwise (local) confounds, for use in ANATICOR-like denoising protocols.
A new interface for 3dReHo enables estimation of voxelwise and ROI-wise regional homogeneity.
The interface for 3dROIstats has been reworked to support a broader range of parameters and regional statistics.

List of changes proposed in this PR (pull-request)

Localstat interface added for AFNI's 3dLocalstat.
ReHo interface added for AFNI's 3dReHo.
ROIstats input spec accepts new parameters: num_roi, zerofill, roisel, debug, nomeanout, nobriklab, format1D, format1DR, and stat. This means that parameters to the ROIstats interface can now be used to specify computation of regional statistics other than the default zero-inclusive mean.
The changes to ROIstats are not backward-compatible; for instance, the output has been renamed from stats to out_file. Software using the existing ROIstats interface will need to be updated accordingly.

Questions

Is backward compatibility or internal naming consistency generally more important? The changes to ROIstats currently favour internal consistency, but it would be no trouble to change the ROIstats interface to be fully backward-compatible instead.

Acknowledgment

(Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

codecov-io · 2018-10-20T03:57:48Z

Codecov Report

Merging #2740 into master will decrease coverage by 3.33%.
The diff coverage is 88%.

@@            Coverage Diff             @@
##           master    #2740      +/-   ##
==========================================
- Coverage   67.42%   64.09%   -3.34%     
==========================================
  Files         340      338       -2     
  Lines       43172    43187      +15     
  Branches     5353     5359       +6     
==========================================
- Hits        29110    27679    -1431     
- Misses      13363    14439    +1076     
- Partials      699     1069     +370

Flag	Coverage Δ
#smoketests	`?`
#unittests	`64.09% <88%> (-0.71%)`	⬇️

Impacted Files	Coverage Δ
nipype/interfaces/afni/__init__.py	`100% <ø> (ø)`	⬆️
nipype/interfaces/afni/preprocess.py	`82.4% <100%> (+1%)`	⬆️
nipype/interfaces/afni/utils.py	`81.89% <83.63%> (+0.14%)`	⬆️
nipype/interfaces/nilearn.py	`40% <0%> (-56.67%)`	⬇️
nipype/utils/spm_docs.py	`25.92% <0%> (-44.45%)`	⬇️
nipype/interfaces/freesurfer/base.py	`49.59% <0%> (-30.9%)`	⬇️
nipype/utils/logger.py	`59.7% <0%> (-29.86%)`	⬇️
nipype/algorithms/rapidart.py	`35.39% <0%> (-29.21%)`	⬇️
nipype/interfaces/spm/base.py	`58.41% <0%> (-29.05%)`	⬇️
nipype/utils/provenance.py	`55.73% <0%> (-28.99%)`	⬇️
... and 49 more

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effigies

This looks good. Thanks for the contribution. A few suggestions.

effigies · 2018-10-25T13:25:58Z

nipype/interfaces/afni/preprocess.py

        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)


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)

effigies · 2018-10-25T13:29:47Z

nipype/interfaces/afni/preprocess.py

+                            'zeromedian': '-median',
+                            'zerosigma': '-sigma',
+                            'zeromode': '-mode'
+                        }


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', ... }

effigies · 2018-10-25T13:31:29Z

nipype/interfaces/afni/utils.py

+    chi_sq = traits.Bool(
+        argstr='-chi_sq',
+        desc='Output the Friedman chi-squared value in addition to the '
+             'Kendall\'s W.')


Should there be an output that's defined when this is True?

effigies · 2018-10-25T13:31:45Z

nipype/interfaces/afni/utils.py

+        argstr='-chi_sq',
+        desc='Output the Friedman chi-squared value in addition to the '
+             'Kendall\'s W.')
+    mask = traits.File(


mask_file for consistency?

effigies · 2018-10-25T13:33:56Z

nipype/interfaces/afni/utils.py

+                            'faces': 7,
+                            'edges': 19,
+                            'vertices': 27,
+                        }


Please reformat this dictionary as above.

effigies · 2018-10-25T13:34:04Z

nipype/interfaces/afni/utils.py

+    output_spec = ReHoOutputSpec
+
+    def _list_outputs(self):
+


No blank line here.

effigies · 2018-10-30T17:37:23Z

@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 · 2018-10-30T19:10:03Z

Thanks!

rciric added 11 commits October 19, 2018 15:59

add 3dLocalstat functionality to support ANATICOR

62d1155

add regional homogeneity interface

494e224

substantially expand functionality of 3dROIstats interface

05c056c

fix Localstat interface

cca5eb2

remove unnecessary dependency; formatting

b0c95e0

new/updated autotests

a8fa089

remove unused dependency

1aee771

update documentation

f66e414

remove escaped line breaks from example cmdline

c2e507f

desc format cleanup

5149267

update convention; use object after all

b7d6871

rciric force-pushed the master branch from f4c61a6 to 446a971 Compare October 20, 2018 03:57

examples fix

426def1

rciric force-pushed the master branch from 446a971 to 426def1 Compare October 20, 2018 04:22

effigies reviewed Oct 25, 2018

View reviewed changes

effigies added this to the 1.1.5 milestone Oct 26, 2018

conform to PEP8, add deprecated field for ROIStats interface

13d7229

effigies modified the milestones: 1.1.5, 1.1.4 Oct 30, 2018

update deprecation

8c65b81

effigies changed the title ~~[ENH] AFNI interfaces: add 3dLocalStat and 3dReHo, rework 3dROIstats~~ [ENH] Add afni.LocalStat and afni.ReHo, update afni.ROIStats inputs Oct 30, 2018

effigies merged commit 50862c1 into nipy:master Oct 30, 2018

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[ENH] Add afni.LocalStat and afni.ReHo, update afni.ROIStats inputs #2740

[ENH] Add afni.LocalStat and afni.ReHo, update afni.ROIStats inputs #2740

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[ENH] Add afni.LocalStat and afni.ReHo, update afni.ROIStats inputs #2740

[ENH] Add afni.LocalStat and afni.ReHo, update afni.ROIStats inputs #2740

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Summary

List of changes proposed in this PR (pull-request)

Questions

Acknowledgment

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