1.4.5

Patch release in the 1.4.x series.

In preparation for fMRIPrep 21.0.0 release.

• FIX: Conform entity ordering to BIDS specification for derivatives (#676)
• ENH: Add CIFTI surface plot (#663)

1.4.4

Release Notes

Patch release in the 1.4.x series.

This release enables better multi-echo handling in fMRIPrep.

CHANGES

• ENH: Return all bold files from init_bold_reference_wf (#673)

1.4.3

Patch Notes

Patch release in the 1.4.x series, including improvements to the carpetplot figure.
With thanks to Zaki A. for the contributions.

Changes

• ENH: Carpet plot tweaks (#617)
• FIX: Patch ants.Registration interface temporarily (#654)
• MAINT: Revise Docker image building and dependencies (#655)
• MAINT: Relax matplotlib constraint (#668)
• MAINT: Configure black to avoid excessive rewriting (#666)

1.4.2

Release Notes

Bug-fix release in the 1.4.x series revising dependencies and including minor improvements to the Docker image, a complete overhaul of the documentation skin, building and deployment & archival.

CHANGES

• DOC: Overhaul - new skin, new deployment & multiversion archival (#656, #657, #658)
• MAINT: Revise Docker image building and dependencies (#655)

Full Changelog: 1.4.1...1.4.2

Maintainers

@mgxd, @effigies, @oesteban

1.4.1

Release Notes

Bug-fix release in the 1.4.x series.

This depends on the latest nitransforms, enabling downstream tools to upgrade.

CHANGES

• FIX: Patch ants.Registration interface temporarily (#654)

1.3.5

Release Notes

Bug-fix release in the 1.3.x series

Changes

• FIX: Set slope and intercept to 1/0 if not otherwise provided (#649)
• FIX: DerivativesDataSink warning when it has multiple source files [backport #573] (#647)
• FIX: FSDetectInputs mutually exclusive options for ReconAll (#646)
• MNT: Update some version pinning and correct for pandas warning about keyword arguments (#645)
• CI: Use datalad-managed test data [BACKPORT] (#653)

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

1.4.0rc6

1.4.0rc6 (May 17, 2021)

* FIX: ``DerivativesDataSink`` dismissing entity writing reportlet (#638)
* 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)
* ENH: Update visual report specification with fieldmaps (#634)
* ENH: Expose the output of the ``ValidateImage`` node as an output in EPI reference workflow (#636)
* DOC: Ensure copyright notice in all headers' comment (#635)
* MAINT: Pin *svgutils* to previous versions (#596)

1.3.3

Release Notes

Bug-fix release in the 1.3.x series.

CHANGES

• FIX: Limit memory usage in EstimateReferenceImage (#629)
• FIX: Check for in_segm input, not seg_file (#592)
• FIX: Use the mask to calculate FOV rather than the fixed image in GenerateSamplingReference (#583)
• FIX: Allow omission of for template normalization (#582)
• MAINT: Pin svgutils to 0.3.1 (#596)
• MAINT: Migrate from Travis -> GH Actions (#589)
• CI: CircleCI housekeeping (#580)

1.4.0rc5

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).

* FIX: Update svgutils after breaking API changes (#620)
* FIX: Address issues with ``RobustAverage`` global signal measurement (#607)
* 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: 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: 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)