fix: skip t1w file existence check if anat_derivatives are provided #545
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
Best reviewed: with all changes
Optimal code review plan (3 commits squashed)
|
bpinsard
force-pushed
the
fix/skip_t1w_check_if_precom_anat
branch
from
2f3931a
to
526ba69
Compare
|
Hello @bpinsard, Thank you for updating! Cheers! There are no style issues detected in this Pull Request. 🍻 To test for issues locally, Comment last updated at 2020-07-01 13:24:43 UTC |
bpinsard
force-pushed
the
fix/skip_t1w_check_if_precom_anat
branch
from
526ba69
to
fc197ca
Compare
Codecov Report
@@ Coverage Diff @@
## master #545 +/- ##
===========================================
- Coverage 64.65% 51.90% -12.75%
===========================================
Files 44 44
Lines 5375 5373 -2
Branches 786 782 -4
===========================================
- Hits 3475 2789 -686
- Misses 1742 2481 +739
+ Partials 158 103 -55
Continue to review full report at Codecov.
|
|
@mgxd Should we target 1.3.0 or 1.2.7 with this? |
|
I think this is fine for either, but since the behavior will not be included into the 20.1.x series of fmriprep, I'm leaning towards 1.3.0 - wdyt? |
|
Sure. I just haven't kept up with the current status of dependencies. Merging into master. |
mgxd
approved these changes
Jul 16, 2020
|
oh, nevermind - it's in 😄 |
|
Suggestion LGTM. Feel free to patch on master. |
oesteban
added a commit
that referenced
this pull request
Aug 14, 2020
First release in the 1.3.x series. This release includes enhancements and bug-fixes towards the release of the first LTS version of fMRIPrep. PyBIDS has been revised to use more recent versions, a series of ANTs' interfaces have been deemed ready to upstream into Nipype, and several improvements regarding multi-echo EPI are included. With thanks to Basile Pinsard for contributions. * FIX: Patch ``ApplyTransforms`` spec to permit identity in a chain (#554) * FIX: Add dots to extensions in PyBIDS' config file (#548) * FIX: Segmentation plots aligned with cardinal axes (#544) * FIX: Skip T1w file existence check if ``anat_derivatives`` are provided (#545) * FIX: Avoid diverting CIFTI dtype from original BOLD (#532) * ENH: Add ``smooth`` input to ``RegridToZooms`` (#549) * ENH: Enable ``DerivativesDataSink`` to take multiple source files to derive entities (#547) * ENH: Allow ``bold_reference_wf`` to accept multiple EPIs/SBRefs (#408) * ENH: Numerical stability of EPI brain-masks using probabilistic prior (#485) * ENH: Add a pure-Python interface to resample to specific resolutions (#511) * MAINT: Finalize upstreaming of ANTs' interfaces to Nipype (#550) * MAINT: Update to Python +3.6 (#541)
HippocampusGirl
added a commit
to HippocampusGirl/niworkflows
that referenced
this pull request
Sep 29, 2020
1.3.0rc3 First release in the 1.3.x series. This release includes enhancements and bug-fixes towards the release of the first LTS version of fMRIPrep. PyBIDS has been revised to use more recent versions, a series of ANTs' interfaces have been deemed ready to upstream into Nipype, and several improvements regarding multi-echo EPI are included. With thanks to Basile Pinsard for contributions. * FIX: Patch ``ApplyTransforms`` spec to permit identity in a chain (nipreps#554) * FIX: Add dots to extensions in PyBIDS' config file (nipreps#548) * FIX: Segmentation plots aligned with cardinal axes (nipreps#544) * FIX: Skip T1w file existence check if ``anat_derivatives`` are provided (nipreps#545) * FIX: Avoid diverting CIFTI dtype from original BOLD (nipreps#532) * ENH: Add ``smooth`` input to ``RegridToZooms`` (nipreps#549) * ENH: Enable ``DerivativesDataSink`` to take multiple source files to derive entities (nipreps#547) * ENH: Allow ``bold_reference_wf`` to accept multiple EPIs/SBRefs (nipreps#408) * ENH: Numerical stability of EPI brain-masks using probabilistic prior (nipreps#485) * ENH: Add a pure-Python interface to resample to specific resolutions (nipreps#511) * MAINT: Finalize upstreaming of ANTs' interfaces to Nipype (nipreps#550) * MAINT: Update to Python +3.6 (nipreps#541)
HippocampusGirl
added a commit
to HippocampusGirl/niworkflows
that referenced
this pull request
Sep 29, 2020
1.3.0 First release in the 1.3.x series. This release includes enhancements and bug-fixes towards the release of the first LTS (*long-term support*) version of *fMRIPrep*. *PyBIDS* has been revised to use more recent versions, a series of ANTs' interfaces have been deemed ready to upstream into *Nipype*, and several improvements regarding multi-echo EPI are included. With thanks to Basile Pinsard for contributions. * FIX: Patch ``ApplyTransforms`` spec to permit identity in a chain (nipreps#554) * FIX: Add dots to extensions in PyBIDS' config file (nipreps#548) * FIX: Segmentation plots aligned with cardinal axes (nipreps#544) * FIX: Skip T1w file existence check if ``anat_derivatives`` are provided (nipreps#545) * FIX: Avoid diverting CIFTI dtype from original BOLD (nipreps#532) * ENH: Add ``smooth`` input to ``RegridToZooms`` (nipreps#549) * ENH: Enable ``DerivativesDataSink`` to take multiple source files to derive entities (nipreps#547) * ENH: Allow ``bold_reference_wf`` to accept multiple EPIs/SBRefs (nipreps#408) * ENH: Numerical stability of EPI brain-masks using probabilistic prior (nipreps#485) * ENH: Add a pure-Python interface to resample to specific resolutions (nipreps#511) * MAINT: Upstream all bug-fixes in the 1.2.9 release * MAINT: Finalize upstreaming of ANTs' interfaces to Nipype (nipreps#550) * MAINT: Update to Python +3.6 (nipreps#541)
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Changes to allow processing dataset without T1w series if
--anat_derivativesare provided.See nipreps/fmriprep#2201