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[ENH] workflow for calculating phasediff from phase images #30

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[ENH] workflow for calculating phasediff from phase images #30

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f325110
FIX: Replace imports from ``nipype.workflows`` with new niflow package
oesteban Oct 10, 2019
1aa6d0f
ENH: Set-up testing framework
oesteban Aug 6, 2019
d3925cc
ENH: Improved fieldmap reportlets
oesteban Aug 6, 2019
5426448
fix(reportlet): set vmax/vmin
oesteban Aug 6, 2019
b24d599
fix(cmap): add transparency to the color range around zero
oesteban Aug 6, 2019
bd214e2
MAINT: Merge ``long_description.rst`` and ``README.rst``
oesteban Aug 6, 2019
04fa33d
ENH: Revise and add tests for the PEPOLAR correction
oesteban Aug 7, 2019
ad370d3
fix(tests): add FS to Dockerfile and improve the CircleCI workflow
oesteban Aug 7, 2019
279786e
docs(pepolar): revise docstrings - close #18 [skip ci]
oesteban Aug 7, 2019
5aa444a
fix: revise FS license setting
oesteban Aug 7, 2019
e4a84e5
fix: store workdir in artifacts and cache
oesteban Aug 8, 2019
63d46b5
fix: miscellaneous fixes
oesteban Aug 9, 2019
4715af1
fix: do not write output of test to func/ and test whether cache is w…
oesteban Aug 13, 2019
3488c37
fix: remove wrong entity setting
oesteban Aug 13, 2019
3f3a1d8
fix: add pytest config to ``setup.cfg``
oesteban Aug 13, 2019
7ae0a09
maint: add ``pip-wheel-metadata`` to ``.gitignore`` [skip ci]
oesteban Oct 2, 2019
fa03f1f
MNT: Use niflow-nipype1-workflows for old nipype.workflows imports
effigies Oct 8, 2019
8804252
MAINT: Fix dependency of ``deploy_pypi`` in the CircleCI workflow [sk…
oesteban Oct 10, 2019
ebed2ae
Rename boldrefs to distortedrefs
mattcieslak Oct 9, 2019
a1ba56b
Update sdcflows/workflows/base.py
mattcieslak Oct 10, 2019
7a004ea
fix: do not mention phase1/2 in base workflow (done in #30)
oesteban Oct 10, 2019
dfb5af9
Merge pull request #41 from mattcieslak/distortedref
oesteban Oct 11, 2019
7f7464b
MAINT: Housekeeping - flake8 errors, settings, etc.
oesteban Nov 7, 2019
5b4cc23
Merge pull request #44 from oesteban/maint/housekeeping
oesteban Nov 8, 2019
4648340
CI: Optimize CircleCI using a local docker registry instead docker sa…
oesteban Nov 8, 2019
f52481a
Merge pull request #45 from oesteban/maint/optimize-circle
oesteban Nov 8, 2019
4ce0224
DOC: Build API documentation [doc versions]
oesteban Nov 7, 2019
e803c5e
enh: update deploy ssh-key [docs versions]
oesteban Nov 9, 2019
3b09b85
fix: sphinxcontrib-versioning package name
oesteban Nov 9, 2019
1c22fbe
docs: force a new run to check [docs versions]
oesteban Nov 9, 2019
1ae3c84
fix: pacify pep8speaks
oesteban Nov 9, 2019
9e42bd4
Merge pull request #43 from oesteban/docs/build-docs
oesteban Nov 9, 2019
0a594df
ENH: Set-up testing framework
oesteban Aug 6, 2019
ce79d7c
start workflow for calculating phasediff from phase images
mattcieslak Aug 17, 2019
9a8fa5a
adopted fsl's subtraction for making a phasediff
mattcieslak Aug 18, 2019
ed7e573
All fmaps share initial and final stages
mattcieslak Aug 20, 2019
16a20a3
add bspline arg to tests
mattcieslak Aug 20, 2019
ae88c09
make spatial kernel size larger for phase1phase2
mattcieslak Aug 20, 2019
24b0b81
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
ceec0d0
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
3ce6aca
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
d210d95
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
f63a467
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
0d77dfb
start workflow for calculating phasediff from phase images
mattcieslak Aug 17, 2019
68c1551
adopted fsl's subtraction for making a phasediff
mattcieslak Aug 18, 2019
2815b74
All fmaps share initial and final stages
mattcieslak Aug 20, 2019
4888c60
add bspline arg to tests
mattcieslak Aug 20, 2019
dada6e9
make spatial kernel size larger for phase1phase2
mattcieslak Aug 20, 2019
cb0844e
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
fefc2a0
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
6f1c892
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
1ab67a2
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
9d4fd2b
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
c219002
Rename b0 to gre
mattcieslak Oct 9, 2019
7a2ccf7
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
3c0c197
MNT: Use niflow-nipype1-workflows for old nipype.workflows imports
effigies Oct 8, 2019
d198141
start workflow for calculating phasediff from phase images
mattcieslak Aug 17, 2019
2bcac82
adopted fsl's subtraction for making a phasediff
mattcieslak Aug 18, 2019
3894610
All fmaps share initial and final stages
mattcieslak Aug 20, 2019
a6c1631
add bspline arg to tests
mattcieslak Aug 20, 2019
674e365
make spatial kernel size larger for phase1phase2
mattcieslak Aug 20, 2019
43449cf
adopted fsl's subtraction for making a phasediff
mattcieslak Aug 18, 2019
5696345
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
59b779d
Rename b0 to gre
mattcieslak Oct 9, 2019
14bca6f
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
390bb6d
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 10, 2019
77024a6
first pass addressing comments
mattcieslak Oct 11, 2019
2e26696
Update sdcflows/workflows/gre.py
mattcieslak Oct 11, 2019
eef154f
Update sdcflows/workflows/gre.py
mattcieslak Oct 11, 2019
907ea7f
Update sdcflows/workflows/phdiff.py
mattcieslak Oct 11, 2019
7e76155
Make specific interface for phase subtraction
mattcieslak Oct 25, 2019
af463aa
Remove duplicated ProcessPhases
mattcieslak Oct 25, 2019
50b6cdc
expand docstrings
mattcieslak Nov 5, 2019
ad88376
enh: double-check the rebase is okay, rewrite some docstrings
oesteban Nov 9, 2019
fe1c51b
fix: make sure docs build
oesteban Nov 9, 2019
5bc2490
Add rebased master branch
mattcieslak Nov 9, 2019
af51019
FIX: Clean up cache and pin latest nipype
oesteban Nov 9, 2019
eaf164b
fix: pull a fresh cache when tag [fresh workdir] is present
oesteban Nov 12, 2019
2df5d44
Merge pull request #47 from oesteban/fix/master
oesteban Nov 12, 2019
3cee196
fix: advance installing the extra key in case it has to be the same a…
oesteban Nov 12, 2019
56c1e30
CI: Add check to avoid deployment of documentation from forks
oesteban Nov 13, 2019
4bc6167
fix: invalid yaml config file for circle
oesteban Nov 13, 2019
5187258
ci: remove docs deploy from master
oesteban Nov 14, 2019
024319e
ci: re-enable docs deploy, enable circleci-artifact-retrieve bot
oesteban Nov 14, 2019
6120938
fix(artifacts-bot): correct path [skip ci]
oesteban Nov 14, 2019
5844e36
DOC: Fix typo and link to BIDS Specification
oesteban Nov 14, 2019
83fb0e7
fix: ordering of docs_deploy jobs
oesteban Nov 14, 2019
0f9933a
Merge pull request #49 from oesteban/docs/fix-minor-typos
oesteban Nov 14, 2019
85d728a
CI: fix configuration
oesteban Nov 14, 2019
f17f0f2
ENH: Set-up testing framework
oesteban Aug 6, 2019
24569aa
start workflow for calculating phasediff from phase images
mattcieslak Aug 17, 2019
2a5facf
adopted fsl's subtraction for making a phasediff
mattcieslak Aug 18, 2019
1c04144
All fmaps share initial and final stages
mattcieslak Aug 20, 2019
a04d251
add bspline arg to tests
mattcieslak Aug 20, 2019
4d71447
make spatial kernel size larger for phase1phase2
mattcieslak Aug 20, 2019
d1c9025
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
34979ad
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
e3e4e67
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
fc0cced
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
342bfdf
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
be442c3
start workflow for calculating phasediff from phase images
mattcieslak Aug 17, 2019
5d80aa9
adopted fsl's subtraction for making a phasediff
mattcieslak Aug 18, 2019
4fa586b
All fmaps share initial and final stages
mattcieslak Aug 20, 2019
56b6b3f
add bspline arg to tests
mattcieslak Aug 20, 2019
51d0f70
make spatial kernel size larger for phase1phase2
mattcieslak Aug 20, 2019
1f8bf88
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
01b5182
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
bf3a1f2
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
d8c99ae
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
8a699c1
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
f29d9c2
Rename b0 to gre
mattcieslak Oct 9, 2019
ec7e8f6
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
55adba3
MNT: Use niflow-nipype1-workflows for old nipype.workflows imports
effigies Oct 8, 2019
2f135c9
start workflow for calculating phasediff from phase images
mattcieslak Aug 17, 2019
99f3c21
adopted fsl's subtraction for making a phasediff
mattcieslak Aug 18, 2019
b4dcf02
All fmaps share initial and final stages
mattcieslak Aug 20, 2019
f9cf651
add bspline arg to tests
mattcieslak Aug 20, 2019
5f544d6
make spatial kernel size larger for phase1phase2
mattcieslak Aug 20, 2019
494de5c
adopted fsl's subtraction for making a phasediff
mattcieslak Aug 18, 2019
4e8c3aa
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
7473a3f
Rename b0 to gre
mattcieslak Oct 9, 2019
de3ffa1
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 3, 2019
5fa6dc2
Update sdcflows/interfaces/fmap.py
mattcieslak Oct 10, 2019
ad40279
first pass addressing comments
mattcieslak Oct 11, 2019
516d4ab
Update sdcflows/workflows/gre.py
mattcieslak Oct 11, 2019
e277463
Update sdcflows/workflows/gre.py
mattcieslak Oct 11, 2019
268eb38
Update sdcflows/workflows/phdiff.py
mattcieslak Oct 11, 2019
257ac65
Make specific interface for phase subtraction
mattcieslak Oct 25, 2019
daf28e8
Remove duplicated ProcessPhases
mattcieslak Oct 25, 2019
22d051c
expand docstrings
mattcieslak Nov 5, 2019
f6cbd0d
enh: double-check the rebase is okay, rewrite some docstrings
oesteban Nov 9, 2019
b3fd5dd
fix: make sure docs build
oesteban Nov 9, 2019
a32778f
Add rebased master branch [fresh workdir]
mattcieslak Nov 9, 2019
19a1a9d
merge from github [skip ci]
mattcieslak Nov 14, 2019
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