0.4.0rc1

What's Changed

🛠 Breaking Changes

• Change default highpass filter cutoff from 0.009 to 0.01 by @kahinimehta in #755
• Refactor anatomical workflow by @tsalo in #706
• Do not require --combineruns to generate DCAN QC files by @tsalo in #753
• Change QC filenames and fix xcp_d-combineqc command-line interface by @tsalo in #762
• Retain cohort entity in derivative filenames by @tsalo in #769
• Require the --cifti flag in order to use --warp-surfaces-native2std by @tsalo in #770
• Zero out parcels with <50% coverage by @tsalo in #757
• Use constant padding and maximum padlen for temporal filtering by @tsalo in #779

🎉 Exciting New Features

• Add option to estimate brain radius from brain mask by @tsalo in #754
• Output warped atlases to derivatives by @tsalo in #647
• Add min_coverage parameter to threshold parcel coverage by @tsalo in #782
• Improve executive summary carpet plots by @tsalo in #747
• Output T2w images if available by @tsalo in #648

🐛 Bug Fixes

• Replace missing vertices' values with NaNs by @tsalo in #743
• Select MNI152NLin6Asym target space for T1w from CIFTI derivatives by @tsalo in #759
• Only generate brainsprite figures when the --dcan_qc flag is used by @tsalo in #766

Other Changes

• Add tests for cifti smoothness by @kahinimehta in #659
• Fix CIFTI downcasting test by @tsalo in #752
• Use pytest to test command-line interface by @tsalo in #740
• Upload coverage reports to CodeCov by @tsalo in #758
• Link to xcp_d-examples in documentation by @tsalo in #761
• Add information about preprocessing requirements by @tsalo in #772
• Replace MultiLabel interpolation with GenericLabel by @tsalo in #786
• Mention cosine regressors in aCompCor boilerplate by @tsalo in #788
• Update base Docker image by @tsalo in #799

Full Changelog: 0.3.2...0.4.0rc1

0.3.3rc4

Full Changelog: 0.3.3rc3...0.3.3rc4

0.3.3rc3

What's Changed

Other Changes

• MAINT 0.3.x: Update base Docker image by @tsalo in #798

Full Changelog: 0.3.3rc2...0.3.3rc3

0.3.3rc2

What's Changed

Other Changes

• Update Dockerfile by @tsalo in #797

Full Changelog: 0.3.3rc1...0.3.3rc2

0.3.3rc1

A release candidate for maintenance of the 0.3.+ series.

What's Changed

Other Changes

• 0.3.x: Change permissions of miniconda folders in Dockerfile by @tsalo in #795

Full Changelog: 0.3.2...0.3.3rc1

0.3.2

This release adopts a workbench show-scene-based brainsprite for the executive summary. It also removes the brainsprite figure from the nipreps report.

What's Changed

🎉 Exciting New Features

• Adopt executive summary's brainsprite using jinja templates by @tsalo in #702

Other Changes

• Remove example data and fix workflow graphs by @tsalo in #738
• Replace CiftiDespike with connected nodes by @tsalo in #737

Full Changelog: 0.3.1...0.3.2

0.3.1

What's Changed

🛠 Breaking Changes

• Remove --nuissance-regressors and --bandpass_filter by @tsalo in #658

🎉 Exciting New Features

• Add --dummy-scans parameter and deprecate --dummytime by @tsalo in #616
• Add --bids-filter-file parameter by @tsalo in #686
• Enable non-aggressive denoising with signal regressors by @tsalo in #697
• Improve identification of FreeSurfer derivatives by @tsalo in #719
• Collect preprocessed surfaces in new function by @tsalo in #731

🐛 Bug Fixes

• Remove dummy volumes from custom confounds files by @tsalo in #660
• Remove dummy volumes from beginning of each run in concatenation workflow by @tsalo in #661
• Retain noise components instead of dropping them in load_aroma by @tsalo in #670
• Use input_type to determine order of preferred spaces by @tsalo in #688
• Infer volumetric space from transform in executive summary with cifti data by @tsalo in #689
• Change input type from HPC to HCP by @kahinimehta in #691
• Replace failing non-aggressive AROMA denoising with working aggressive denoising by @tsalo in #693
• Select best volumetric space for transforms even when using --cifti flag by @tsalo in #695
• Downcast >32-bit files to 32-bit by @tsalo in #666
• Use appropriate intent codes for cifti outputs by @tsalo in #690
• Only concatenate processed runs by @tsalo in #713
• Do not use downcasted files as name sources by @tsalo in #712
• Warp segmentation file to appropriate space for carpet plots by @tsalo in #727
• Use brain mask in NIFTI connectivity workflow by @tsalo in #733

Other Changes

• Consolidate confounds at beginning of denoising workflows by @tsalo in #664
• Remove unused outputnodes from nifti and cifti workflows by @tsalo in #667
• Move QC/censoring plots into new workflow by @tsalo in #668
• Testing affines don't change across XCP runs by @kahinimehta in #649
• Load confounds via Nilearn functionality by @kahinimehta in #675
• Update docs by @kahinimehta in #682
• Add masks to package data by @kahinimehta in #715
• Use ds001491 fMRIPrep derivatives for tests by @tsalo in #698
• Add tests for confound loading function by @tsalo in #730
• Refactor executive summary workflow by @tsalo in #721
• Track start of workflow with sentry by @tsalo in #732

Full Changelog: 0.3.0...0.3.1

0.3.0

We are happy to announce a new minor release, with several backwards-incompatible changes.

Two big breaking changes are (1) there is a new --dcan-qc flag that determines if the executive summary and DCAN-format QC files will be generated, and (2) custom confounds should now have headers, should be tab-delimited, and should have the same names as the fMRIPrep confounds, for easier indexing.

What's Changed

🛠 Breaking Changes

• Output ReHo as a CIFTI by @tsalo in #601
• Add --dcan-qc flag by @tsalo in #650
• Support custom confounds with headers by @tsalo in #642

🎉 Exciting New Features

• Use BIDSLayout in concatenation code by @tsalo in #600
• [ENH] Support Nibabies ingression into XCP by @kahinimehta in #602
• Add static ALFF and ReHo plots to report by @kahinimehta in #604
• Write confounds out to derivatives by @kahinimehta in #634
• Add column names to confounds df by @kahinimehta in #641

🐛 Bug Fixes

• Select BOLD files in a single space by @tsalo in #603
• Censor data in executive summary plots correctly by @kahinimehta in #614
• Only generate ALFF derivatives if bandpass filtering is enabled by @tsalo in #628
• Do not merge in concatenated files when re-running concatenation workflow by @tsalo in #633
• Map abbreviated entities to full names for templateflow get call by @tsalo in #654
• Ensure dummyscans is an integer in PlotSVGData by @tsalo in #655

Other Changes

• Use Nilearn for brainsprite generation by @tsalo in #607
• Cache the downloaded test data by @tsalo in #629
• Use BIDSLayout instead of globbing functions to collect necessary files by @tsalo in #621
• Start to standardize interface parameter calls by @tsalo in #638
• Simplify transform-getting functions by @tsalo in #623
• Lint with black without linting workflow connections by @tsalo in #640

Full Changelog: 0.2.0...0.3.0

0.2.2

This is a patch release for the 0.2 series. The main bug being fixed is that using --dummytime was causing crashes in the executive summary workflow.

What's Changed

🎉 Exciting New Features

• Write confounds out to derivatives by @kahinimehta in #634
• Add column names to confounds df by @kahinimehta in #641

🐛 Bug Fixes

• Do not merge in concatenated files when re-running concatenation workflow by @tsalo in #633
• Map abbreviated entities to full names for templateflow get call by @tsalo in #654
• Ensure dummyscans is an integer in PlotSVGData by @tsalo in #655

Other Changes

• Cache the downloaded test data by @tsalo in #629
• Use BIDSLayout instead of globbing functions to collect necessary files by @tsalo in #621
• Start to standardize interface parameter calls by @tsalo in #638
• Simplify transform-getting functions by @tsalo in #623
• Lint with black without linting workflow connections by @tsalo in #640

Full Changelog: 0.2.1...0.2.2

0.2.1

This is a patch release for 0.2.0.

There is a known bug with the concatenation workflow, so we advise users not to use the -m/--combineruns option with this release.

What's Changed

🛠 Breaking Changes

• Output ReHo as a CIFTI by @tsalo in #601

🎉 Exciting New Features

• Use BIDSLayout in concatenation code by @tsalo in #600
• [ENH] Support Nibabies ingression into XCP by @kahinimehta in #602
• Add static ALFF and ReHo plots to report by @kahinimehta in #604

🐛 Bug Fixes

• Select BOLD files in a single space by @tsalo in #603
• Censor data in executive summary plots correctly by @kahinimehta in #614
• Only generate ALFF derivatives if bandpass filtering is enabled by @tsalo in #628

Other Changes

• Use Nilearn for brainsprite generation by @tsalo in #607

Full Changelog: 0.2.0...0.2.1