From 2209cd601827037c31e3eed485c3e4c7c486c049 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Mon, 8 Feb 2021 13:41:58 -0800 Subject: [PATCH] rel(1.4.0rc4): Update CHANGES [skip ci] --- CHANGES.rst | 60 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) diff --git a/CHANGES.rst b/CHANGES.rst index fa92d0610ab..280de595cbd 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -5,6 +5,8 @@ This release includes enhancements and bug-fixes towards the release of the firs 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). @@ -22,12 +24,70 @@ them: *NiRodents* and *NiBabies* (and their corresponding *fMRIPrep* extensions) A list of prominent changes follows: +* 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 ```` 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: 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) +.. caution:: + + 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`` + 1.3.2 (November 5, 2020) ======================== Bug-fix release in the 1.3.x series.