1.4.0

Release Notes

First release in the 1.4.x series.
This release includes enhancements and bug-fixes towards the release of the first
beta version of dMRIPrep.
It also contains new features that are necessary for the API overhaul that has
happened within the new SDCFlows 2.x series.
The new series include a cross-cutting (modalities, species) workflow to generate
EPI references.
Finally other NiPreps will also have a first release with specific support for
them: NiRodents and NiBabies (and their corresponding fMRIPrep extensions).

⚠️ NiWorkflows has been relicensed! ⚠️
As of the first release candidate of the 1.4 series, the license has changed
from BSD 3-clause to the Apache License 2.0.
Amongst several terms that are changing, the following two premises are relevant
if you derive code from the new series:
* You must give any other recipients of the Work or Derivative Works a copy
of this License; and
* You must cause any modified files to carry prominent notices stating that
You changed the files.

A list of prominent changes can be found below. (With thanks to Lea Waller for the contributions)

Changes

• DOC: Ensure copyright notice in all headers' comment (#635)
• FIX: Set slope and intercept to 1/0 if not otherwise provided (#649)
• FIX: DerivativesDataSink warning when it has multiple source files (#647)
• FIX: FSDetectInputs mutually exclusive options for ReconAll (#646)
• FIX: Remove pandas warning about use of keyword arguments (#645)
• FIX: Improve SimpleBeforeAfterRPT contour visibility (#643)
• FIX: DerivativesDataSink dismissing entity writing reportlet (#638)
• FIX: Ensure IntensityClip input is a 3D file (#621)
• FIX: Limit memory usage in EstimateReferenceImage (#629)
• FIX: Purge removed --disable flag from svgo call (#626)
• FIX: Readd sbref_file input to reference volume interface (#624)
• FIX: Update svgutils after breaking API changes (#620)
• FIX: Address issues with RobustAverage global signal measurement (#607)
• FIX: NonsteadyStatesDetector wrongly using Nipype's is_outlier (#605)
• FIX: Change in svgutils' API on 0.3.2 breaks reportlets (#599)
• FIX: Check for in_segm input, not seg_file (typo) (#592)
• FIX: Use the mask to calculate FOV rather than the fixed image in GenerateSamplingReference (#583)
• FIX: Allow omission of <res> for template normalization (#582)
• FIX: Include _T2starw _MTw and _TSE-suffixes in build_path options (#584)
• FIX: DerivativesDataSink warning when it has multiple source files (#573)
• ENH: Allow SimpleBeforeAfterRPT plotting of image rotated to cardinal axes (#650)
• ENH: Update visual report specification with fieldmaps (#634)
• ENH: Expose the output of the ValidateImage node as an output in EPI reference workflow (#636)
• ENH: Add an inversion operation to IntensityClip (#616)
• ENH: Cross-cutting (modalities, species) workflow to generate EPI references (#610)
• ENH: Add a RobustAverage interface and split volume selection (#602)
• ENH: Revise some patterns of the BIDSLayout config to aid SDCFlows new API (#585)
• ENH: Upstream fMRIPrep's init_bbreg_wf to integrate it in dMRIPrep (#586)
• MAINT: Pin svgutils to previous versions (#596)
• MAINT: Drop gh-pages history, reducing repository size (#622)
• MAINT: Add DS030 dataset, with clipped (55 timepoints) BOLD data (#609)
• MAINT: Migrate ds003_downsampled to nipreps-data (#608)
• MAINT: Move mask-regressions test-data to datalad + nipreps-data (#606)
• MAINT: Refactor structure of interfaces (#603)
• MAINT: Drop Python 3.6, test setuptools builds, pip installations, and revise Docker pinned versions (#593)
• MAINT: CircleCI housekeeping (#580)
• RF: Write derivatives once, using deterministic gzip settings (#641)

⚠️ API Changes ⚠️
The niworkflows.interfaces submodule has been refactored.
To migrate from previous series, please modify the following imports:
* images.MatchHeader -> header.MatchHeader
* images.ValidateImage -> header.ValidateImage
* images.Demean -> nibabel.Demean
* images.FilledImageLike -> nibabel.FilledImageLike
* images.RegridToZooms -> nibabel.RegridToZooms
* masks.ROIsPlot -> reportlets.masks.ROIsPlot
* masks.ComputeEPIMask -> nilearn.ComputeEPIMask
* mni.RobustMNINormalization -> norm.SpatialNormalization
* New niworkflows.interfaces.reportlets submodule
* report_base -> reportlets.base
* masks -> reportlets.masks
* registration -> reportlets.registration
* segmentation -> reportlets.segmentation
* utils.GenerateSamplingReference -> nibabel.GenerateSamplingReference
* utils.CopyXForm -> header.CopyXForm
* utils.NormalizeMotionParams -> confounds.NormalizeMotionParams
* utils.AddTPMs -> probmaps.AddTPMs
* utils.TPM2ROI -> probmaps.TPM2ROI
* utils.AddTSVHeader -> utility.AddTSVHeader
* utils.JoinTSVColumns -> utility.JoinTSVColumns
* utils.DictMerge -> utility.DictMerge
* utils.TSV2JSON -> utility.TSV2JSON
Beware that interface aliases at the top niworkflows.interfaces level have
been removed:
* ExpandModel, SpikeRegressors from confounds
* BET -> reportlets.masks.BETRPT
* FAST -> reportlets.segmentation.FASTRPT
* FLIRT, ApplyXFM, RobustMNINormalization, Registration,
ApplyTransforms, SimpleBeforeAfter now under reportlets.registration
as FLIRTRPT, ApplyXFMRPT, RobustMNINormalizationRPT, ANTSRegistrationRPT,
ANTSApplyTransformsRPT, SimpleBeforeAfterRPT.
* CopyXForm, CopyHeader, SanitizeImage now under header
* NormalizeMotionParams now under confounds.
* FMRISummary, CompCorVariancePlot, ConfoundsCorrelationPlot from plotting