0.10.6

What's Changed

🎉 Exciting New Features

• Add session-id parameter by @tsalo in #1379
• Add colorbar to correlation matrix plot by @tsalo in #1401

🐛 Bug Fixes

• Support --abcc-qc with --file-format nifti by @tsalo in #1388
• Do not attempt to concatenate runs when no runs in entity set are processed by @tsalo in #1398
• Make calculations robust to NaNs by @tsalo in #1399
• Fix atlas names in concatenated parcellated output files by @tsalo in #1407

Other Changes

• Only estimate head radius if necessary by @tsalo in #1381
• Simplify the brainsprite workflow setup by @tsalo in #1384
• Parallelize image denoising by @mattcieslak in #1387
• Apply consistency across XCP-D quick-start instructions by @singlesp in #1382
• Test PlotSlicesForBrainSprite by @tsalo in #1393
• Update mode documentation by @B-Sevchik in #1392
• Add comments and debug logging to init_denoise_bold_wf by @tientong98 in #1391
• Add more OMP by @mattcieslak in #1386
• Note that automatic head radius estimation gives higher values than 50 by @tsalo in #1397
• Add file lock to avoid concurrent edits by @tientong98 in #1403
• Clarify mounting in apptainer instructions by @singlesp in #1394

New Contributors

• @singlesp made their first contribution in #1382
• @B-Sevchik made their first contribution in #1392
• @tientong98 made their first contribution in #1391

Full Changelog: 0.10.5...0.10.6

0.10.5

What's Changed

🎉 Exciting New Features

• Use trimesh to generate brainsprite by @tsalo in #1368

🐛 Bug Fixes

• Stop autoescaping the boilerplate by @mattcieslak in #1369

Full Changelog: 0.10.4...0.10.5

0.10.4

What's Changed

🐛 Bug Fixes

• Support multi-step composite transforms from Nibabies by @tsalo in #1365

Full Changelog: 0.10.3...0.10.4

0.10.3

This release fixes a testing bug that prevented 0.10.2 from deploying.

What's Changed

🐛 Bug Fixes

• Allow sub- prefix in participant labels by @tsalo in #1347
• Downgrade connectome workbench version by @tsalo in #1358
• Fix resource class of CIFTI tests by @tsalo in #1362

Other Changes

• Clarify that warped surfaces can be overlaid on the MNI152NLin6Asym template by @tsalo in #1349
• Run ruff by @tsalo in #1357

Full Changelog: 0.10.1...0.10.3

0.10.2

This release failed to deploy due a testing issue, so please skip forward to 0.10.3.

What's Changed

🐛 Bug Fixes

• Downgrade connectome workbench version by @tsalo in #1358
• Allow sub- prefix in participant labels by @tsalo in #1347

Other Changes

• Clarify that warped surfaces can be overlaid on the MNI152NLin6Asym template by @tsalo in #1349
• Run ruff by @tsalo in #1357

Full Changelog: 0.10.1...0.10.2

0.10.1

A patch release fixing bugs stemming from 0.10.0.

What's Changed

🐛 Bug Fixes

• Write out correlations when --create-matrices doesn't include "all" by @tsalo in #1326
• Use confounds file with non-steady-state columns to identify dummy volumes by @tsalo in #1330

Other Changes

• Document the nichart mode by @tsalo in #1325
• Update indexed-gzip requirement from ~=1.8.7 to ~=1.9.1 by @dependabot in #1327

Full Changelog: 0.10.0...0.10.1

0.10.0

This backwards-incompatible release brings XCP-D further in line with the fMRIPost workflows in the NiPreps ecosystem.
We have added the ability to provide custom confound sets defined as YAML config files,
ingress derivatives from fMRIPost BIDS Apps (for example, fMRIPost-AROMA),
and provide external atlases organized as BIDS-Atlas datasets.

Please note that the BIDS-Atlas extension proposal has not been merged into BIDS yet,
so the expected organization of these external atlas datasets may change over time.

What's Changed

🛠 Breaking Changes

• Replace restricted confound sets with config files by @tsalo in #1255
• Rename --derivatives parameter to --datasets by @tsalo in #1276
• Accept external atlases by searching BIDS-Atlas datasets by @tsalo in #1265
• Move hemi entity before space by @tsalo in #1287

🎉 Exciting New Features

• Remove Freesurfer node from surface normalization workflow by @tsalo in #1273
• Track Sources with BIDSURI interface by @tsalo in #1283
• Add nichart mode by @tsalo in #1320

🐛 Bug Fixes

• Patch task_id into bids_filters by @tsalo in #1271
• Fix NIfTI-surface connection by @tsalo in #1284
• Update build image version by @tsalo in #1293
• Fix bug with surfaces and external atlases by @tsalo in #1304
• Apply notch filter appropriate number of times based on --motion-filter-order by @tsalo in #1300
• Fix ingression of standard-space mesh files by @tsalo in #1309
• Fix init_qc_report_wf connections when linc-qc and abcc-qc are disabled by @tsalo in #1314

Other Changes

• Don't rerun alff if num threads changes by @mattcieslak in #1263
• Remove xcp_d_dir and clean datasinks by @tsalo in #1262
• Add dataset links to config object by @tsalo in #1266
• Document minimal required inputs by @tsalo in #1270
• Correct documentation regarding Freesurfer by @tsalo in #1277
• Improve custom confound documentation by @tsalo in #1280
• Improve documentation of new features by @tsalo in #1281
• Use ruff for linting by @tsalo in #1312
• Fix links to documentation by @tsalo in #1323

Full Changelog: 0.9.1...0.10.0

0.10.0rc3

What's Changed

🐛 Bug Fixes

• Apply notch filter appropriate number of times based on --motion-filter-order by @tsalo in #1300
• Fix ingression of standard-space mesh files by @tsalo in #1309

Full Changelog: 0.10.0rc2...0.10.0rc3

0.10.0rc2

What's Changed

🛠 Breaking Changes

• Move hemi entity before space by @tsalo in #1287

🎉 Exciting New Features

• Track Sources with BIDSURI interface by @tsalo in #1283

🐛 Bug Fixes

• Fix NIfTI-surface connection by @tsalo in #1284
• Update build image version by @tsalo in #1293
• Fix bug with surfaces and external atlases by @tsalo in #1304

Other Changes

• Improve documentation of new features by @tsalo in #1281

Full Changelog: 0.10.0rc1...0.10.0rc2

0.10.0rc1

What's Changed

🛠 Breaking Changes

• Replace restricted confound sets with config files by @tsalo in #1255
• Rename --derivatives parameter to --datasets by @tsalo in #1276
• Accept external atlases by searching BIDS-Atlas datasets by @tsalo in #1265

🎉 Exciting New Features

• Remove Freesurfer node from surface normalization workflow by @tsalo in #1273

🐛 Bug Fixes

• Patch task_id into bids_filters by @tsalo in #1271

Other Changes

• Don't rerun alff if num threads changes by @mattcieslak in #1263
• Remove xcp_d_dir and clean datasinks by @tsalo in #1262
• Add dataset links to config object by @tsalo in #1266
• Document minimal required inputs by @tsalo in #1270
• Correct documentation regarding Freesurfer by @tsalo in #1277
• Improve custom confound documentation by @tsalo in #1280

Full Changelog: 0.9.1...0.10.0rc1