0.5.0rc1

This release prepares for the XCP-D paper.

In the next release, we will replace the Schaefer atlases with AtlasPack combined Schaefer-subcortical atlases.

What's Changed

🛠 Breaking Changes

• Add CIFTI subcortical atlas to XCP-D by @tsalo in #864

🎉 Exciting New Features

• Refactor dcan/hcp ingestion and add more surface files by @tsalo in #887
• Add "none" option for denoising by @tsalo in #879
• Add --exact-time parameter by @tsalo in #885
• Allow white matter surface suffix to be either "_smoothwm" or "_white" by @tsalo in #899
• Add --fs-license-file parameter to command line interface by @tsalo in #930

🐛 Bug Fixes

• Standardize executive summary carpet if params is "none" by @tsalo in #916
• Support CIFTI morphometry files and add PNC test data by @tsalo in #922
• Correct ABCD/HCP surface ingression by @tsalo in #927

Other Changes

• Improve QC sidecar contents by @tsalo in #900
• Rename the parcellated ALFF/ReHo outputs by @tsalo in #902
• Remove workaround for nonbinary Nibabies brain masks by @tsalo in #905
• Update Landing Page Figure by @kahinimehta in #908
• Remove unused functions in filemanip module by @tsalo in #911
• Add tests for xcp_d.utils.utils module by @tsalo in #910
• Add tests for xcp_d.utils.execsummary module by @tsalo in #912
• Expand tests by @tsalo in #913
• Test CLI parameter validation by @tsalo in #918
• Refactor collection functions by @tsalo in #917

Full Changelog: 0.4.1rc2...0.5.0rc1

0.4.1rc2

What's Changed

Other Changes

• Fix description of signal denoising method in docs by @tsalo in #898

Full Changelog: 0.4.1rc1...0.4.1rc2

0.4.1rc1

This release candidate comes after overhauling XCP-D's packaging. I've made the release to test the updated Docker image.

What's Changed

🎉 Exciting New Features

• Write out top-level sidecar for PennLINC QC file by @tsalo in #894
• Parcellate ReHo, ALFF, and surface morphometric maps by @tsalo in #839

Other Changes

• Add contributing documentation by @tsalo in #893
• Update changelog and CFF file for 0.4.0 by @tsalo in #896
• Change packaging to use hatch-vcs and pyproject.toml by @tsalo in #897

Full Changelog: 04.0...0.4.1rc1

0.4.0

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
• Replace non-aggressive denoising with orthogonalization and streamline denoising by @tsalo in #808
• Add design matrix to report by @tsalo in #824
• Write out censored results by @tsalo in #820
• Allow users to disable censoring, and only generate ALFF if censoring is disabled by @tsalo in #828
• Implement --min-time parameter by @tsalo in #836
• Remove deprecated --dummytime parameter by @tsalo in #837
• Change FD Threshold from 0.2 to 0.3 by @kahinimehta in #854
• Use filtered motion in nuisance regression by @tsalo in #871

🎉 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
• Generate CIFTI and TSV versions of coverage, timeseries, and correlation files by @tsalo in #785
• Add colorbar to executive summary carpet plots by @tsalo in #829
• Support fsLR-space shape files generated by preprocessing pipelines by @tsalo in #773
• Support preprocessing derivatives with T2w, but no T1w by @tsalo in #838
• Support high-pass or low-pass only filtering by @smeisler in #862

🐛 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
• Check for existence of dataset_description.json in fmri_dir by @tsalo in #806
• Move dataset desc check to after conversion by @tsalo in #809
• Refactor HCP/DCAN ingression and fix converted filenames by @tsalo in #714
• Connect custom confounds to confound consolidation node by @tsalo in #835
• Work around load_confounds aCompCor bug by @tsalo in #851
• Allow for smoothing to be zero by @tsalo in #861
• Use appropriate T1w/T2w in brainsprite workflow by @tsalo in #860
• Test DCAN and HCP ingestion and fix related bugs by @tsalo in #848

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
• Document Singularity requirements by @tsalo in #805
• Use workflow nodes for workflow tests by @tsalo in #807
• Adjust code for niworkflows 1.7.3 by @tsalo in #810
• Use a workflow for concatenation by @tsalo in #821
• Create prepare_confounds and denoise_bold workflows by @tsalo in #827
• Simplify the anatomical workflow some more by @tsalo in #841
• Remove codecov dependency by @tsalo in #850
• Add boilerplate to the executive summary by @tsalo in #857
• Add additional argument aliases by @smeisler in #870
• Update docs to mention HCPYA version by @kahinimehta in #869
• Improve boilerplate by @tsalo in #866
• Update gitignore by @tsalo in #874
• Fix issues with HCP Ingression by @kahinimehta in #872
• Document how to process multiple, but not all, tasks by @tsalo in #876
• Describe scope of XCP-D by @tsalo in #878
• Update docs by @kahinimehta in #882
• Always generate the DCAN executive summary by @tsalo in #888
• Clean up testing framework and documentation by @tsalo in #889

Full Changelog: 0.3.2...04.0

0.4.0rc2

What's Changed

🛠 Breaking Changes

• Replace non-aggressive denoising with orthogonalization and steamline denoising by @tsalo in #808
• Add design matrix to report by @tsalo in #824
• Write out censored results by @tsalo in #820
• Allow users to disable censoring, and only generate ALFF if censoring is disabled by @tsalo in #828

🎉 Exciting New Features

• Generate CIFTI and TSV versions of coverage, timeseries, and correlation files by @tsalo in #785

🐛 Bug Fixes

• Check for existence of dataset_description.json in fmri_dir by @tsalo in #806
• Move dataset desc check to after conversion by @tsalo in #809
• Refactor HCP/DCAN ingression and fix converted filenames by @tsalo in #714

Other Changes

• Document Singularity requirements by @tsalo in #805
• Use workflow nodes for workflow tests by @tsalo in #807
• Adjust code for niworkflows 1.7.3 by @tsalo in #810
• Use a workflow for concatenation by @tsalo in #821
• Create prepare_confounds and denoise_bold workflows by @tsalo in #827

Full Changelog: 0.4.0rc1...0.4.0rc2

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