ENH: b0 reference and skullstrip workflow #50

@@            Coverage Diff             @@
##           master      #50      +/-   ##
==========================================
- Coverage   55.51%   52.37%   -3.15%     
==========================================
  Files          11       16       +5     
  Lines         762      907     +145     
  Branches      110      114       +4     
==========================================
+ Hits          423      475      +52     
- Misses        338      431      +93     
  Partials        1        1

Impacted Files	Coverage Δ
dmriprep/interfaces/reports.py	`60.71% <ø> (-0.4%)`	⬇️
dmriprep/workflows/dwi/__init__.py	`100% <100%> (ø)`
dmriprep/config/__init__.py	`100% <100%> (ø)`	⬆️
dmriprep/workflows/base.py	`29.57% <25%> (-1.31%)`	⬇️
dmriprep/workflows/dwi/util.py	`27.02% <27.02%> (ø)`
dmriprep/workflows/dwi/outputs.py	`38.46% <38.46%> (ø)`
dmriprep/interfaces/images.py	`41.17% <41.17%> (ø)`
dmriprep/workflows/dwi/base.py	`41.66% <41.66%> (ø)`
... and 3 more

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oesteban

Had a quick pass so that you can get things moving along

dmriprep/interfaces/images.py

initial port from niworkflows add initial pre-mask step fix doc add pre_mask address review comments add period extract b0s first fix function name typo initial port from niworkflows add initial pre-mask step fix doc add pre_mask address review comments add period extract b0s first fix function name typo remove MatchHeader

Co-Authored-By: Oscar Esteban <code@oscaresteban.es>

josephmje · 2020-01-15T14:32:18Z

@oesteban thanks for hacking on this! new report! https://458-174237413-gh.circle-artifacts.com/0/tmp/THP002/derivatives/dmriprep/sub-THP0005.html

oesteban · 2020-01-15T16:47:44Z

I tried a fix to the niworkflows problem and then rolled back. I'm going to go for it. Thanks for this precious contribution!

oesteban reviewed Jan 14, 2020

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josephmje and others added 26 commits January 14, 2020 22:38

Update dmriprep/workflows/dwi/util.py

854ab59

Co-Authored-By: Oscar Esteban <code@oscaresteban.es>

Update dmriprep/interfaces/images.py

c4be8f9

Co-Authored-By: Oscar Esteban <code@oscaresteban.es>

Update dmriprep/interfaces/images.py

7d34342

Co-Authored-By: Oscar Esteban <code@oscaresteban.es>

update to use inputs according to #26

d93d6c8

initial b0 registration adapted from niworkflows

69e3bd5

fix masking

76371f7

update docs and doctests

f0453b9

add workflow test

4707fb2

add pytest fixtures

baec874

docs: revise docstrings for napoleon parsing

8e558eb

add mcflirt and fix rescale_b0 inputs and outputs

86223a8

fix imputs again

db804f9

joining gradtable and skullstrip

11670a6

add fake metadata for docs

2bd4402

fix typo

db7d2d0

remove outputs file

1cdadd0

add summary and validation datasinks

aef46db

fix layout grabbing

1a7c147

fix doctests

b9278ef

fix flake8 issues

aab7d6d

ordering is sensitive to spaces

387de45

add fake files for docs

441f83e

add missing arg

2ae0326

add missing arg

aad8eae

fix docstring

15fd36f

josephmje and others added 15 commits January 14, 2020 22:38

fix doctests

0af3425

fix typos

c04c4d2

Apply suggestions from code review

09e196f

Co-Authored-By: Oscar Esteban <code@oscaresteban.es>

address Oscar's comments

b705c0e

fix tests

62ab4b1

remove automodules

f15ac0a

enh: connect workflow

34283f9

fix: enable execution of the diffusion workflow

720e9e1

fix: various nodes failing

ece13e1

fix: amend previous commit - left bad connection name

e56cc3f

fix: amend previous commit - left bad connection name

fb9a635

fix: remove diffusionsummary

072ce05

enh: split out reports to a new module

286ab00

sty: fix all dunder

83e86a9

fix indentation in reports config

51da317

oesteban merged commit c695f4c into nipreps:master Jan 15, 2020

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ENH: b0 reference and skullstrip workflow #50

ENH: b0 reference and skullstrip workflow #50

josephmje commented Jan 13, 2020

pull-assistant bot commented Jan 13, 2020 •

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pep8speaks commented Jan 13, 2020 •

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josephmje commented Jan 15, 2020

oesteban commented Jan 15, 2020

ENH: b0 reference and skullstrip workflow #50

ENH: b0 reference and skullstrip workflow #50

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josephmje commented Jan 13, 2020

pull-assistant bot commented Jan 13, 2020 • edited

pep8speaks commented Jan 13, 2020 • edited

Comment last updated at 2020-01-15 16:46:44 UTC

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josephmje commented Jan 15, 2020

oesteban commented Jan 15, 2020

pull-assistant bot commented Jan 13, 2020 •

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