0.9.0

Release Notes

A number of new features and bugfixes. This release includes a refactor of the reports generation system that attempts to better generalize to other BIDS-Apps. The new reports internally use pybids to find reportlets, and the configuration file has been migrated to YAML to allow line breaks when captioning reportlets. The release also provides more infrastructure for fMRIPrep and sMRIPrep, including some BIDS-related interfaces.

CHANGES

• ENH: Miscellaneous improvements to the Reports (#357) @oesteban
• ENH: Add a KeySelect interface (#347) @oesteban
• FIX: BusError in DerivativesDataSink (#356) @effigies
• FIX: GenerateSamplingReference failed extension with #348 (#354) @oesteban
• FIX: Revise tests after sloppy merge of #352 (#353) @oesteban
• FIX: Reportlets path and output path were wrong (#352) @oesteban
• FIX: Use safe loader for YAML data input in reports (#351) @oesteban
• FIX: Allow native grids (i.e. pass-through) for GenerateSamplingReference (#348) @oesteban
• ENH: Add new confounds model to reports template (#349) @oesteban
• ENH/FIX: Migrate default config to YAML, fix ROIs query. (#346) @oesteban
• REL: Synchronization with latest fMRIPrep changes + minor improvements (#345) @oesteban
• ENH: DerivativesDataSink now accepts metadata dictionaries too (#332) @oesteban
• ENH: Upstream init_gifti_surface_wf from sMRIPrep (#328) @oesteban
• FIX: Do not generate 4D references out of 4D single-band references (SBRefs) (#338) @oesteban
• FIX: Allow pipelining dynamic outputs of ReadSidecarJSON (#340) @oesteban
• ENH: Dictionary manipulation / TSV to dict, merge multiple dicts (#341) @rciric
• ENH: Run a second N4BiasFieldCorrection node to refine INU correction (#342) @oesteban
• ENH: Add an allowed_entities setting in DerivativesDataSink (#343) @oesteban
• ENH: Refactor of the Report generation tools (#344) @oesteban
• PIN: Update dependencies - nilearn!=0.5.0,!=0.5.1 and latest templateflow (0.1.7)

0.9.0a2

Release Notes

Finally fixed the problem holding the sMRIPrep release - the new data files needed to be listed in the MANIFEST.in file.

CHANGES

• ENH/FIX: Migrate default config to YAML, fix ROIs query. (#346) @oesteban

0.9.0a1

Release Notes

Hotfixes over the previous pre-release.

CHANGES

• REL: Synchronization with latest fMRIPrep changes + minor improvements (#345) @oesteban

0.9.0a0

Release Notes

A number of new features, mostly making BIDS-related interfaces more enjoyable
and including a large refactor of the reports factory that now internally uses
pybids to find reportlets.

CHANGES

• ENH: DerivativesDataSink now accepts metadata dictionaries too (#332) @oesteban
• ENH: Upstream init_gifti_surface_wf from sMRIPrep (#328) @oesteban
• FIX: Do not generate 4D references out of 4D single-band references (SBRefs) (#338) @oesteban
• FIX: Allow pipelining dynamic outputs of ReadSidecarJSON (#340) @oesteban
• ENH: Dictionary manipulation / TSV to dict, merge multiple dicts (#341) @rciric
• ENH: run a second N4BiasFieldCorrection node to refine INU correction (#342) @oesteban
• ENH: Add an allowed_entities setting in DerivativesDataSink (#343) @oesteban
• ENH: Refactor of the Report generation tools (#344) @oesteban
• PIN: Update dependencies - nilearn!=0.5.0,!=0.5.1 and latest TemplateFlow (0.1.7)

0.8.2

Release Notes

New release to go along with the upcoming MRIQC 0.15.0.

CHANGES

• ENH: Update CompCor plotting to allow getting NaNs (#326) @rciric
• ENH: Ensure brain mask's conformity (#324) @oesteban
• ENH: Add several helper interfaces (#325) @oesteban
• FIX: "NONE of the components..." banner was printed even when no AROMA file was present (#330) @oesteban

0.8.1

Release Notes

Niworkflows 0.8.1 ships with a fully-Nipype brain extraction workflow, dual to ANTs' antsBrainExtraction.sh. TemplateFlow has been updated to enable using MNI152NLin2009cAsym as target template. Additionally, the DerivativesDataSink interface has been supercharged with the possibility of writing sidecar JSON files. That will enable the rapid adoption of BIDS-Derivatives by fMRIPrep and sMRIPrep.

CHANGES

• FIX: Revising antsBrainExtraction dual workflow (#316) @oesteban
• ENH: Expose bias-corrected T1w before skull-stripping (#317) @oesteban
• ENH: DerivativesDataSink - enable JSON sidecar writing (#318) @oesteban

0.8.0

Release Notes

This release starts series 0.8, characterized for including TemplateFlow series 0.1 (which is now independent of datalad and queried with pybids).

CHANGES

• [PIN] Update to TemplateFlow 0.1.0 (#315) @oesteban

0.7.2

Release Notes

Fixes to some edge cases and improved confound calculation/reporting.

CHANGES

• [FIX] Do not cast run BIDS-entity to string (#307) @oesteban
• [FIX] Scaling of confound fix (#310) @wiheto
• [FIX] GenerateSamplingReference with correct zooms (#312) @effigies
• [ENH] AROMA plots - add warning for edge cases (none/all are noise) (#292) @jdkent
• [ENH] Confound enhancement (#287) @rciric

0.7.1.post1

Release Notes

A quick hotfix to a minor issue derived from the refactor in BIDS interfaces

CHANGES

• [FIX] Do not cast run BIDS-entity to string (#307) @oesteban

0.7.1

Release Notes

Releasing some minimal improvements over the previous release.

CHANGES

• [TST] Add test on BIDSInfo interface (#302) @oesteban
• [MNT] Deprecate getters module (#305) @oesteban
• [FIX] Improve bounding box computation from masks (#304) @oesteban