0.9.0

This backwards-incompatible makes two important breaking changes. First, we changd the default file format for 'linc' mode from NIfTI to CIFTI. Second, XCP-D no longer ingresses and warps the anatomical tissue segmentation file (*_dseg.nii.gz), since no one was using it and it's easy enough to collect separately.

Additionally, this release fixes a bug with the collection of sphere files needed to warp fsnative surfaces to fsLR space, which should only affect derivatives from fMRIPrep and Nibabies versions >= 24.0.0 (i.e., versions that include space-fsnative in the spheres' filenames).

What's Changed

🛠 Breaking Changes

• Change linc mode default file format to CIFTI by @tsalo in #1248
• Stop ingressing anatomical-space tissue segmentation file by @tsalo in #1190

🎉 Exciting New Features

• Internally support voxel-wise confounds by @tsalo in #1244

🐛 Bug Fixes

• Fix subject sphere query by @tsalo in #1249

Full Changelog: 0.8.3...0.9.0

0.8.3

This patch release fixes a bug introduced in 0.8.1.

What's Changed

🐛 Bug Fixes

• Fix collection in case of derivatives with T1w and T2w but T1w is primary by @tsalo in #1240

Other Changes

• Document how to request a new mode by @tsalo in #1238

Full Changelog: 0.8.2...0.8.3

0.8.2

This release adds the "none" option for the mode parameter.

What's Changed

🎉 Exciting New Features

• Implement "none" mode by @tsalo in #1232

🐛 Bug Fixes

• Account for floating point issues in ALFF time array creation by @tsalo in #1236

Full Changelog: 0.8.1...0.8.2

0.8.1

Patch release for HBCD to support Nibabies runs with both T1w and T2w data.

What's Changed

🐛 Bug Fixes

• Explicitly check for -p none and --custom-confounds by @tsalo in #1222

Other Changes

• Restructure XCP-D to better match fMRIPrep by @tsalo in #1225
• Document the apptainer version requirements by @tsalo in #1233
• Make collect_data work for T1w+T2w nibabies derivatives by @tsalo in #1234

Full Changelog: 0.8.0...0.8.1

0.8.0

This is a backwards-incompatible release that will be used to postprocess the beta version of the first release of the HBCD dataset.
There are two major breaking changes.
First, there is a new required --mode parameter that automatically defines sets of parameters to match recommendations from different studies/labs.
Each parameter that the --mode parameter controls can be overridden, so users should be able to reproduce their original settings from previous versions of XCP-D.
Second, XCP-D now loads certain sphere files from the BIDS derivatives, rather than non-BIDS Freesurfer or MCRIBS folders.
This means that the anatomical workflow (--warp-surfaces-native2std) will only work for fMRIPrep versions >= 23.1.0 and Nibabies versions >= 23.1.0.
The rest of XCP-D should still work for versions of fMRIPrep and Nibabies that were supported previously, but we cannot guarantee this.

What's Changed

🛠 Breaking Changes

• Add required --mode parameter to define sets of parameters by @tsalo in #1109
• Load spheres for anatomical workflow from TemplateFlow and BIDS derivatives by @tsalo in #1207

🎉 Exciting New Features

• Add discretized MID-B and Myers-Labonte atlases by @tsalo in #1192
• Plot CIFTI maps on subject-specific surfaces when available by @tsalo in #1208
• Allow bids-filter-file terms for mesh and morphometry files by @tsalo in #1210

🐛 Bug Fixes

• Generate session-wise executive summaries by @tsalo in #1202
• Look for space entity in T2w-only anatomical inputs by @tsalo in #1203
• Use standard-space anatomical brain mask by @tsalo in #1204
• Drop volumetric Myers-Labonte atlas by @tsalo in #1212
• Enable linc-qc for abcd and hbcd modes by default by @tsalo in #1220

Other Changes

• Document anatomical workflow in more detail by @tsalo in #1191
• Fix up documentation by @tsalo in #1209
• Reorganize QC interfaces by @tsalo in #1215
• Allow space-fsaverage for sphere files by @tsalo in #1217
• Continue to improve documentation of anatomical workflow by @tsalo in #1216

Full Changelog: 0.7.5...0.8.0

0.7.5

This is a patch release that fixes how the correlation matrix plot is generated when users select only one atlas for parcellation.

What's Changed

🐛 Bug Fixes

• Fix ConnectPlot by @tsalo in #1188

Other Changes

• Refactor CIFTI parcellation and connectivity workflows to use wb_command by @tsalo in #1174
• Replace internal smoothing spheres with ones from TemplateFlow by @tsalo in #1160

Full Changelog: 0.7.4...0.7.5

0.7.4

This is a patch release that fixes two important bugs. The two bugs are: (1) band-pass filter values were not respected in versions 0.7.1 - 0.7.3 (they were hardcoded to 0.01 - 0.1) and (2) when processing CIFTI files, parcellated ReHo values in TSVs were not correct, due to a problem with how we were reconstructing CIFTI ReHo files. The dense CIFTI files should still be useable though.

What's Changed

🎉 Exciting New Features

• Make ConnectPlot robust to chosen atlases by @tsalo in #1161

🐛 Bug Fixes

• Fix band-pass filter settings in Config by @tsalo in #1172
• Allow ALFF to work with low-pass or high-pass filters by @tsalo in #1176
• Use CiftiCreateDenseFromTemplate for CIFTI ReHo by @tsalo in #1175

Other Changes

• Use nireports for HTML report generation by @tsalo in #1169

Full Changelog: 0.7.3...0.7.4

0.7.3

Small patch release for manuscript's executive summary.

What's Changed

🐛 Bug Fixes

• Drop concatenated rest-as-run section from executive summary by @tsalo in #1156

Full Changelog: 0.7.2...0.7.3

0.7.2

This is a patch release fixing small bugs in 0.7.1.

What's Changed

🎉 Exciting New Features

• Make GeneratedBy in preprocessing derivatives' dataset_description.json optional by @tsalo in #1151

🐛 Bug Fixes

• Fix exit code bug in cli.run.main() by @tsalo in #1152

Other Changes

• Replace pkgrf with load_data by @tsalo in #1147
• Update to new build image (v0.0.12) by @tsalo in #1153

Full Changelog: 0.7.1...0.7.2

0.7.1

This release prepares for the XCP-D manuscript.

What's Changed

🛠 Breaking Changes

• Change default --min-time from 100 to 240 by @tsalo in #1115

🎉 Exciting New Features

• Add --bids-database-dir parameter by @tsalo in #1116
• Ignore subcortical figures and plot FOV center of reference brains in executive summary by @tsalo in #1145

🐛 Bug Fixes

• Modify metadata and boilerplate to reflect updated motion filter parameters by @tsalo in #1114
• Add "subject" to native-space surface query by @tsalo in #1118
• Stop using config.nipype.memory_gb as memory limit in workflow nodes by @tsalo in #1122
• Pin dependencies to fix RTD build by @tsalo in #1136
• Fix adjacency matrix for CIFTI ReHo by @tsalo in #1120
• Use run-specific cwd for UK Biobank ingression interface by @tsalo in #1137
• Add third config to BIDSLayout that defines cohort entity by @tsalo in #1143
• Use standardized DVARS from Nipype by @tsalo in #1135

Other Changes

• Adopt Nipreps-style Config object by @tsalo in #1040
• Use pytest-env to capture warnings on CI runs by @tsalo in #1107
• Convert coverage values to float32 to address pandas warning by @tsalo in #1112
• Only describe the atlases selected by the user by @tsalo in #1126
• Fix API documentation by @tsalo in #1144
• Improve denoising tests by @tsalo in #1146

Full Changelog: 0.7.0...0.7.1