Releases | Open Source Science

What's Changed

🐛 Bug Fixes

Fix figure collection for longitudinal, but not session-wise, reports by @tsalo in https://github.com/PennLINC/xcp_d/pull/1482 ### Other Changes
Drop dir and run entities from single-run tasks by @tsalo in https://github.com/PennLINC/xcp_d/pull/1472
Check DatasetType for "derivative" or "derivatives" by @tsalo in https://github.com/PennLINC/xcp_d/pull/1481

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.11.0...0.11.1

- Python
Published by tsalo 7 months ago

What's Changed

🛠 Breaking Changes

Use mem_mb instead of mem_gb by @smeisler in https://github.com/PennLINC/xcp_d/pull/1417 ### 🎉 Exciting New Features
Add --report-output-level parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/1436
Collect and apply transforms between native anatomical spaces by @tsalo in https://github.com/PennLINC/xcp_d/pull/1437 ### 🐛 Bug Fixes
Ensure T1w-only processing does not collect T2w by @tsalo in https://github.com/PennLINC/xcp_d/pull/1433
Support session-wise anatomical processing by @tsalo in https://github.com/PennLINC/xcp_d/pull/1438
Fix session-wise collection by @tsalo in https://github.com/PennLINC/xcp_d/pull/1439
Fix session-wise collection of surface files by @tsalo in https://github.com/PennLINC/xcp_d/pull/1440
Make workflow name unique for session-wise processing by @tsalo in https://github.com/PennLINC/xcp_d/pull/1441
Add nifti brain mask to hcpya ingression by @smeisler in https://github.com/PennLINC/xcp_d/pull/1411
Write out filtered motion parameters when dummy-scans is not zero by @tsalo in https://github.com/PennLINC/xcp_d/pull/1446
Ingress BOLD brain mask in ABCD-BIDS and HCP processing by @tsalo in https://github.com/PennLINC/xcp_d/pull/1473 ### Other Changes
Update note about HCP compatibility by @tsalo in https://github.com/PennLINC/xcp_d/pull/1465

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.10.7...0.11.0

- Python
Published by tsalo 7 months ago

This release introduces one minor breaking change (--mem-gb has become --mem-mb), but other than that it's mostly a bug-fix release that will now leverage session-wise anatomical data, when available (e.g., for Nibabies derivatives).

What's Changed

🛠 Breaking Changes

Use mem_mb instead of mem_gb by @smeisler in https://github.com/PennLINC/xcp_d/pull/1417 ### 🎉 Exciting New Features
Add --report-output-level parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/1436
Collect and apply transforms between native anatomical spaces by @tsalo in https://github.com/PennLINC/xcp_d/pull/1437 ### 🐛 Bug Fixes
Ensure T1w-only processing does not collect T2w by @tsalo in https://github.com/PennLINC/xcp_d/pull/1433
Support session-wise anatomical processing by @tsalo in https://github.com/PennLINC/xcp_d/pull/1438
Fix session-wise collection by @tsalo in https://github.com/PennLINC/xcp_d/pull/1439
Fix session-wise collection of surface files by @tsalo in https://github.com/PennLINC/xcp_d/pull/1440
Make workflow name unique for session-wise processing by @tsalo in https://github.com/PennLINC/xcp_d/pull/1441
Add nifti brain mask to hcpya ingression by @smeisler in https://github.com/PennLINC/xcp_d/pull/1411

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.10.7...0.11.0rc1

- Python
Published by tsalo 10 months ago

xcp_d - 0.10.7

What's Changed

🎉 Exciting New Features

Use masked functional and anatomical images for executive summary by @tsalo in https://github.com/PennLINC/xcp_d/pull/1425 ### 🐛 Bug Fixes
Warp fsLR surfaces to NLin6 for brainsprite by @tsalo in https://github.com/PennLINC/xcp_d/pull/1419
Warp anat mask to anat space for coreg QC by @tsalo in https://github.com/PennLINC/xcp_d/pull/1423
Remove background label in ConnectPlot by @tsalo in https://github.com/PennLINC/xcp_d/pull/1424 ### Other Changes
Run vertex normalization on output surfaces by @tsalo in https://github.com/PennLINC/xcp_d/pull/1420

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.10.6...0.10.7

- Python
Published by tsalo 11 months ago

xcp_d - 0.10.6

What's Changed

🎉 Exciting New Features

Add session-id parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/1379
Add colorbar to correlation matrix plot by @tsalo in https://github.com/PennLINC/xcp_d/pull/1401 ### 🐛 Bug Fixes
Support --abcc-qc with --file-format nifti by @tsalo in https://github.com/PennLINC/xcp_d/pull/1388
Do not attempt to concatenate runs when no runs in entity set are processed by @tsalo in https://github.com/PennLINC/xcp_d/pull/1398
Make calculations robust to NaNs by @tsalo in https://github.com/PennLINC/xcp_d/pull/1399
Fix atlas names in concatenated parcellated output files by @tsalo in https://github.com/PennLINC/xcp_d/pull/1407 ### Other Changes
Only estimate head radius if necessary by @tsalo in https://github.com/PennLINC/xcp_d/pull/1381
Simplify the brainsprite workflow setup by @tsalo in https://github.com/PennLINC/xcp_d/pull/1384
Parallelize image denoising by @mattcieslak in https://github.com/PennLINC/xcp_d/pull/1387
Apply consistency across XCP-D quick-start instructions by @singlesp in https://github.com/PennLINC/xcp_d/pull/1382
Test PlotSlicesForBrainSprite by @tsalo in https://github.com/PennLINC/xcp_d/pull/1393
Update mode documentation by @B-Sevchik in https://github.com/PennLINC/xcp_d/pull/1392
Add comments and debug logging to initdenoiseboldwf by @tientong98 in https://github.com/PennLINC/xcpd/pull/1391
Add more OMP by @mattcieslak in https://github.com/PennLINC/xcp_d/pull/1386
Note that automatic head radius estimation gives higher values than 50 by @tsalo in https://github.com/PennLINC/xcp_d/pull/1397
Add file lock to avoid concurrent edits by @tientong98 in https://github.com/PennLINC/xcp_d/pull/1403
Clarify mounting in apptainer instructions by @singlesp in https://github.com/PennLINC/xcp_d/pull/1394

New Contributors

@singlesp made their first contribution in https://github.com/PennLINC/xcp_d/pull/1382
@B-Sevchik made their first contribution in https://github.com/PennLINC/xcp_d/pull/1392
@tientong98 made their first contribution in https://github.com/PennLINC/xcp_d/pull/1391

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.10.5...0.10.6

- Python
Published by tsalo 12 months ago

xcp_d - 0.10.5

What's Changed

🎉 Exciting New Features

Use trimesh to generate brainsprite by @tsalo in https://github.com/PennLINC/xcp_d/pull/1368 ### 🐛 Bug Fixes
Stop autoescaping the boilerplate by @mattcieslak in https://github.com/PennLINC/xcp_d/pull/1369

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.10.4...0.10.5

- Python
Published by tsalo about 1 year ago

xcp_d - 0.10.4

What's Changed

🐛 Bug Fixes

Support multi-step composite transforms from Nibabies by @tsalo in https://github.com/PennLINC/xcp_d/pull/1365

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.10.3...0.10.4

- Python
Published by tsalo about 1 year ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/1347
Downgrade connectome workbench version by @tsalo in https://github.com/PennLINC/xcp_d/pull/1358
Fix resource class of CIFTI tests by @tsalo in https://github.com/PennLINC/xcp_d/pull/1362 ### Other Changes
Clarify that warped surfaces can be overlaid on the MNI152NLin6Asym template by @tsalo in https://github.com/PennLINC/xcp_d/pull/1349
Run ruff by @tsalo in https://github.com/PennLINC/xcp_d/pull/1357

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.10.1...0.10.3

- Python
Published by tsalo about 1 year ago

xcp_d - 0.10.2

What's Changed

🐛 Bug Fixes

Downgrade connectome workbench version by @tsalo in https://github.com/PennLINC/xcp_d/pull/1358
Allow sub- prefix in participant labels by @tsalo in https://github.com/PennLINC/xcp_d/pull/1347

Other Changes

Clarify that warped surfaces can be overlaid on the MNI152NLin6Asym template by @tsalo in https://github.com/PennLINC/xcp_d/pull/1349
Run ruff by @tsalo in https://github.com/PennLINC/xcp_d/pull/1357

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.10.1...0.10.2

- Python
Published by tsalo about 1 year ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/1326
Use confounds file with non-steady-state columns to identify dummy volumes by @tsalo in https://github.com/PennLINC/xcp_d/pull/1330 ### Other Changes
Document the nichart mode by @tsalo in https://github.com/PennLINC/xcp_d/pull/1325
Update indexed-gzip requirement from ~=1.8.7 to ~=1.9.1 by @dependabot in https://github.com/PennLINC/xcp_d/pull/1327

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.10.0...0.10.1

- Python
Published by tsalo over 1 year ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/1255
Rename --derivatives parameter to --datasets by @tsalo in https://github.com/PennLINC/xcp_d/pull/1276
Accept external atlases by searching BIDS-Atlas datasets by @tsalo in https://github.com/PennLINC/xcp_d/pull/1265
Move hemi entity before space by @tsalo in https://github.com/PennLINC/xcp_d/pull/1287 ### 🎉 Exciting New Features
Remove Freesurfer node from surface normalization workflow by @tsalo in https://github.com/PennLINC/xcp_d/pull/1273
Track Sources with BIDSURI interface by @tsalo in https://github.com/PennLINC/xcp_d/pull/1283
Add nichart mode by @tsalo in https://github.com/PennLINC/xcp_d/pull/1320 ### 🐛 Bug Fixes
Patch taskid into bidsfilters by @tsalo in https://github.com/PennLINC/xcp_d/pull/1271
Fix NIfTI-surface connection by @tsalo in https://github.com/PennLINC/xcp_d/pull/1284
Update build image version by @tsalo in https://github.com/PennLINC/xcp_d/pull/1293
Fix bug with surfaces and external atlases by @tsalo in https://github.com/PennLINC/xcp_d/pull/1304
Apply notch filter appropriate number of times based on --motion-filter-order by @tsalo in https://github.com/PennLINC/xcp_d/pull/1300
Fix ingression of standard-space mesh files by @tsalo in https://github.com/PennLINC/xcp_d/pull/1309
Fix initqcreportwf connections when linc-qc and abcc-qc are disabled by @tsalo in https://github.com/PennLINC/xcpd/pull/1314 ### Other Changes
Don't rerun alff if num threads changes by @mattcieslak in https://github.com/PennLINC/xcp_d/pull/1263
Remove xcpddir and clean datasinks by @tsalo in https://github.com/PennLINC/xcp_d/pull/1262
Add dataset links to config object by @tsalo in https://github.com/PennLINC/xcp_d/pull/1266
Document minimal required inputs by @tsalo in https://github.com/PennLINC/xcp_d/pull/1270
Correct documentation regarding Freesurfer by @tsalo in https://github.com/PennLINC/xcp_d/pull/1277
Improve custom confound documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/1280
Improve documentation of new features by @tsalo in https://github.com/PennLINC/xcp_d/pull/1281
Use ruff for linting by @tsalo in https://github.com/PennLINC/xcp_d/pull/1312
Fix links to documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/1323

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.9.1...0.10.0

- Python
Published by tsalo over 1 year ago

xcp_d - 0.10.0rc3

What's Changed

🐛 Bug Fixes

Apply notch filter appropriate number of times based on --motion-filter-order by @tsalo in https://github.com/PennLINC/xcp_d/pull/1300
Fix ingression of standard-space mesh files by @tsalo in https://github.com/PennLINC/xcp_d/pull/1309

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.10.0rc2...0.10.0rc3

- Python
Published by tsalo over 1 year ago

xcp_d - 0.10.0rc2

What's Changed

🛠 Breaking Changes

Move hemi entity before space by @tsalo in https://github.com/PennLINC/xcp_d/pull/1287 ### 🎉 Exciting New Features
Track Sources with BIDSURI interface by @tsalo in https://github.com/PennLINC/xcp_d/pull/1283 ### 🐛 Bug Fixes
Fix NIfTI-surface connection by @tsalo in https://github.com/PennLINC/xcp_d/pull/1284
Update build image version by @tsalo in https://github.com/PennLINC/xcp_d/pull/1293
Fix bug with surfaces and external atlases by @tsalo in https://github.com/PennLINC/xcp_d/pull/1304 ### Other Changes
Improve documentation of new features by @tsalo in https://github.com/PennLINC/xcp_d/pull/1281

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.10.0rc1...0.10.0rc2

- Python
Published by tsalo over 1 year ago

xcp_d - 0.10.0rc1

What's Changed

🛠 Breaking Changes

Replace restricted confound sets with config files by @tsalo in https://github.com/PennLINC/xcp_d/pull/1255
Rename --derivatives parameter to --datasets by @tsalo in https://github.com/PennLINC/xcp_d/pull/1276
Accept external atlases by searching BIDS-Atlas datasets by @tsalo in https://github.com/PennLINC/xcp_d/pull/1265 ### 🎉 Exciting New Features
Remove Freesurfer node from surface normalization workflow by @tsalo in https://github.com/PennLINC/xcp_d/pull/1273 ### 🐛 Bug Fixes
Patch taskid into bidsfilters by @tsalo in https://github.com/PennLINC/xcp_d/pull/1271 ### Other Changes
Don't rerun alff if num threads changes by @mattcieslak in https://github.com/PennLINC/xcp_d/pull/1263
Remove xcpddir and clean datasinks by @tsalo in https://github.com/PennLINC/xcp_d/pull/1262
Add dataset links to config object by @tsalo in https://github.com/PennLINC/xcp_d/pull/1266
Document minimal required inputs by @tsalo in https://github.com/PennLINC/xcp_d/pull/1270
Correct documentation regarding Freesurfer by @tsalo in https://github.com/PennLINC/xcp_d/pull/1277
Improve custom confound documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/1280

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.9.1...0.10.0rc1

- Python
Published by tsalo over 1 year ago

xcp_d - 0.9.1

This release improves performance with multi-core processing.

What's Changed

Other Changes

Remove nprocs for nodes that do not use multiple cores by @tsalo in https://github.com/PennLINC/xcpd/pull/1256
Remove unused data files by @tsalo in https://github.com/PennLINC/xcp_d/pull/1259
Parallelize ALFF by @tsalo in https://github.com/PennLINC/xcp_d/pull/1258
Replace internal data module with acres by @tsalo in https://github.com/PennLINC/xcp_d/pull/1260

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.9.0...0.9.1

- Python
Published by tsalo over 1 year ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/1248
Stop ingressing anatomical-space tissue segmentation file by @tsalo in https://github.com/PennLINC/xcp_d/pull/1190

🎉 Exciting New Features

Internally support voxel-wise confounds by @tsalo in https://github.com/PennLINC/xcp_d/pull/1244

🐛 Bug Fixes

Fix subject sphere query by @tsalo in https://github.com/PennLINC/xcp_d/pull/1249

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.8.3...0.9.0

- Python
Published by tsalo over 1 year ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/1240 ### Other Changes
Document how to request a new mode by @tsalo in https://github.com/PennLINC/xcp_d/pull/1238

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.8.2...0.8.3

- Python
Published by tsalo over 1 year ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/1232 ### 🐛 Bug Fixes
Account for floating point issues in ALFF time array creation by @tsalo in https://github.com/PennLINC/xcp_d/pull/1236

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.8.1...0.8.2

- Python
Published by tsalo over 1 year ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/1222 ### Other Changes
Restructure XCP-D to better match fMRIPrep by @tsalo in https://github.com/PennLINC/xcp_d/pull/1225
Document the apptainer version requirements by @tsalo in https://github.com/PennLINC/xcp_d/pull/1233
Make collectdata work for T1w+T2w nibabies derivatives by @tsalo in https://github.com/PennLINC/xcpd/pull/1234

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.8.0...0.8.1

- Python
Published by tsalo over 1 year ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/1109
Load spheres for anatomical workflow from TemplateFlow and BIDS derivatives by @tsalo in https://github.com/PennLINC/xcp_d/pull/1207

🎉 Exciting New Features

Add discretized MID-B and Myers-Labonte atlases by @tsalo in https://github.com/PennLINC/xcp_d/pull/1192
Plot CIFTI maps on subject-specific surfaces when available by @tsalo in https://github.com/PennLINC/xcp_d/pull/1208
Allow bids-filter-file terms for mesh and morphometry files by @tsalo in https://github.com/PennLINC/xcp_d/pull/1210

🐛 Bug Fixes

Generate session-wise executive summaries by @tsalo in https://github.com/PennLINC/xcp_d/pull/1202
Look for space entity in T2w-only anatomical inputs by @tsalo in https://github.com/PennLINC/xcp_d/pull/1203
Use standard-space anatomical brain mask by @tsalo in https://github.com/PennLINC/xcp_d/pull/1204
Drop volumetric Myers-Labonte atlas by @tsalo in https://github.com/PennLINC/xcp_d/pull/1212
Enable linc-qc for abcd and hbcd modes by default by @tsalo in https://github.com/PennLINC/xcp_d/pull/1220

Other Changes

Document anatomical workflow in more detail by @tsalo in https://github.com/PennLINC/xcp_d/pull/1191
Fix up documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/1209
Reorganize QC interfaces by @tsalo in https://github.com/PennLINC/xcp_d/pull/1215
Allow space-fsaverage for sphere files by @tsalo in https://github.com/PennLINC/xcp_d/pull/1217
Continue to improve documentation of anatomical workflow by @tsalo in https://github.com/PennLINC/xcp_d/pull/1216

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.7.5...0.8.0

- Python
Published by tsalo over 1 year ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/1188 ### Other Changes
Refactor CIFTI parcellation and connectivity workflows to use wbcommand by @tsalo in https://github.com/PennLINC/xcpd/pull/1174
Replace internal smoothing spheres with ones from TemplateFlow by @tsalo in https://github.com/PennLINC/xcp_d/pull/1160

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.7.4...0.7.5

- Python
Published by tsalo over 1 year ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/1161

🐛 Bug Fixes

Fix band-pass filter settings in Config by @tsalo in https://github.com/PennLINC/xcp_d/pull/1172
Allow ALFF to work with low-pass or high-pass filters by @tsalo in https://github.com/PennLINC/xcp_d/pull/1176
Use CiftiCreateDenseFromTemplate for CIFTI ReHo by @tsalo in https://github.com/PennLINC/xcp_d/pull/1175

Other Changes

Use nireports for HTML report generation by @tsalo in https://github.com/PennLINC/xcp_d/pull/1169

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.7.3...0.7.4

- Python
Published by tsalo over 1 year ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/1156

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.7.2...0.7.3

- Python
Published by tsalo almost 2 years ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/1151 ### 🐛 Bug Fixes
Fix exit code bug in cli.run.main() by @tsalo in https://github.com/PennLINC/xcp_d/pull/1152 ### Other Changes
Replace pkgrf with loaddata by @tsalo in https://github.com/PennLINC/xcpd/pull/1147
Update to new build image (v0.0.12) by @tsalo in https://github.com/PennLINC/xcp_d/pull/1153

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.7.1...0.7.2

- Python
Published by tsalo almost 2 years ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/1115 ### 🎉 Exciting New Features
Add --bids-database-dir parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/1116
Ignore subcortical figures and plot FOV center of reference brains in executive summary by @tsalo in https://github.com/PennLINC/xcp_d/pull/1145 ### 🐛 Bug Fixes
Modify metadata and boilerplate to reflect updated motion filter parameters by @tsalo in https://github.com/PennLINC/xcp_d/pull/1114
Add "subject" to native-space surface query by @tsalo in https://github.com/PennLINC/xcp_d/pull/1118
Stop using config.nipype.memory_gb as memory limit in workflow nodes by @tsalo in https://github.com/PennLINC/xcp_d/pull/1122
Pin dependencies to fix RTD build by @tsalo in https://github.com/PennLINC/xcp_d/pull/1136
Fix adjacency matrix for CIFTI ReHo by @tsalo in https://github.com/PennLINC/xcp_d/pull/1120
Use run-specific cwd for UK Biobank ingression interface by @tsalo in https://github.com/PennLINC/xcp_d/pull/1137
Add third config to BIDSLayout that defines cohort entity by @tsalo in https://github.com/PennLINC/xcp_d/pull/1143
Use standardized DVARS from Nipype by @tsalo in https://github.com/PennLINC/xcp_d/pull/1135 ### Other Changes
Adopt Nipreps-style Config object by @tsalo in https://github.com/PennLINC/xcp_d/pull/1040
Use pytest-env to capture warnings on CI runs by @tsalo in https://github.com/PennLINC/xcp_d/pull/1107
Convert coverage values to float32 to address pandas warning by @tsalo in https://github.com/PennLINC/xcp_d/pull/1112
Only describe the atlases selected by the user by @tsalo in https://github.com/PennLINC/xcp_d/pull/1126
Fix API documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/1144
Improve denoising tests by @tsalo in https://github.com/PennLINC/xcp_d/pull/1146

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.7.0...0.7.1

- Python
Published by tsalo almost 2 years ago

xcp_d - 0.7.1rc6

What's Changed

🛠 Breaking Changes

Change default --min-time from 100 to 240 by @tsalo in https://github.com/PennLINC/xcp_d/pull/1115 ### 🎉 Exciting New Features
Add --bids-database-dir parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/1116 ### 🐛 Bug Fixes
Modify metadata and boilerplate to reflect updated motion filter parameters by @tsalo in https://github.com/PennLINC/xcp_d/pull/1114
Add "subject" to native-space surface query by @tsalo in https://github.com/PennLINC/xcp_d/pull/1118
Stop using config.nipype.memory_gb as memory limit in workflow nodes by @tsalo in https://github.com/PennLINC/xcp_d/pull/1122
Pin dependencies to fix RTD build by @tsalo in https://github.com/PennLINC/xcp_d/pull/1136
Fix adjacency matrix for CIFTI ReHo by @tsalo in https://github.com/PennLINC/xcp_d/pull/1120
Use run-specific cwd for UK Biobank ingression interface by @tsalo in https://github.com/PennLINC/xcp_d/pull/1137 ### Other Changes
Adopt Nipreps-style Config object by @tsalo in https://github.com/PennLINC/xcp_d/pull/1040
Use pytest-env to capture warnings on CI runs by @tsalo in https://github.com/PennLINC/xcp_d/pull/1107
Convert coverage values to float32 to address pandas warning by @tsalo in https://github.com/PennLINC/xcp_d/pull/1112
Only describe the atlases selected by the user by @tsalo in https://github.com/PennLINC/xcp_d/pull/1126

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.7.0...0.7.1rc6

- Python
Published by tsalo almost 2 years ago

xcp_d - 0.7.1rc5

What's Changed

🛠 Breaking Changes

Change default --min-time from 100 to 240 by @tsalo in https://github.com/PennLINC/xcp_d/pull/1115 ### 🎉 Exciting New Features
Add --bids-database-dir parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/1116 ### 🐛 Bug Fixes
Modify metadata and boilerplate to reflect updated motion filter parameters by @tsalo in https://github.com/PennLINC/xcp_d/pull/1114
Add "subject" to native-space surface query by @tsalo in https://github.com/PennLINC/xcp_d/pull/1118
Stop using config.nipype.memory_gb as memory limit in workflow nodes by @tsalo in https://github.com/PennLINC/xcp_d/pull/1122 ### Other Changes
Adopt Nipreps-style Config object by @tsalo in https://github.com/PennLINC/xcp_d/pull/1040
Use pytest-env to capture warnings on CI runs by @tsalo in https://github.com/PennLINC/xcp_d/pull/1107
Convert coverage values to float32 to address pandas warning by @tsalo in https://github.com/PennLINC/xcp_d/pull/1112

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.7.0...0.7.1rc5

- Python
Published by tsalo almost 2 years ago

xcp_d - 0.7.1rc4

What's Changed

🛠 Breaking Changes

Change default --min-time from 100 to 240 by @tsalo in https://github.com/PennLINC/xcp_d/pull/1115 ### 🎉 Exciting New Features
Add --bids-database-dir parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/1116 ### 🐛 Bug Fixes
Modify metadata and boilerplate to reflect updated motion filter parameters by @tsalo in https://github.com/PennLINC/xcp_d/pull/1114
Add "subject" to native-space surface query by @tsalo in https://github.com/PennLINC/xcp_d/pull/1118 ### Other Changes
Adopt Nipreps-style Config object by @tsalo in https://github.com/PennLINC/xcp_d/pull/1040
Use pytest-env to capture warnings on CI runs by @tsalo in https://github.com/PennLINC/xcp_d/pull/1107
Convert coverage values to float32 to address pandas warning by @tsalo in https://github.com/PennLINC/xcp_d/pull/1112

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.7.0...0.7.1rc4

- Python
Published by tsalo almost 2 years ago

xcp_d - 0.7.1rc3

What's Changed

Other Changes

Adopt Nipreps-style Config object by @tsalo in https://github.com/PennLINC/xcp_d/pull/1040
Use pytest-env to capture warnings on CI runs by @tsalo in https://github.com/PennLINC/xcp_d/pull/1107

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.7.0...0.7.1rc3

- Python
Published by tsalo almost 2 years ago

xcp_d - 0.7.1rc2

What's Changed

Other Changes

Adopt Nipreps-style Config object by @tsalo in https://github.com/PennLINC/xcp_d/pull/1040

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.7.0...0.7.1rc2

- Python
Published by tsalo almost 2 years ago

xcp_d - 0.7.1rc1

What's Changed

Other Changes

Adopt Nipreps-style Config object by @tsalo in https://github.com/PennLINC/xcp_d/pull/1040

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.7.0...0.7.1rc1

- Python
Published by tsalo almost 2 years ago

xcp_d - 0.7.0

This is a large, backwards-incompatible release. The changes in this release mostly stem from reviewer comments on the XCP-D manuscript.

I expect to release 0.7.1, which will add the NiPreps Config object, very soon.

What's Changed

🛠 Breaking Changes

[DCAN] Remove --dcan-qc parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/1096
Bring outputs up to date with BEPs 11, 12, 17, and 38 by @tsalo in https://github.com/PennLINC/xcp_d/pull/1065
Stop appending "xcpd" to output directory by @tsalo in https://github.com/PennLINC/xcpd/pull/1061 ### 🎉 Exciting New Features
Create reformatted BrainSwipes figures for HBCD QC by @tsalo in https://github.com/PennLINC/xcp_d/pull/1091 ### Other Changes
Add information about ReHo to read-the-docs by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/1097
Update landing page figure by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/1099
Add band over censored volumes in executive summary carpet plots by @tsalo in https://github.com/PennLINC/xcp_d/pull/1077
Fix image link by @psychelzh in https://github.com/PennLINC/xcp_d/pull/1100

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.6.4...0.7.0

- Python
Published by tsalo almost 2 years ago

xcp_d - 0.7.0rc1

What's Changed

🛠 Breaking Changes

[DCAN] Remove --dcan-qc parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/1096
Bring outputs up to date with BEPs 11, 12, 17, and 38 by @tsalo in https://github.com/PennLINC/xcp_d/pull/1065
Stop appending "xcpd" to output directory by @tsalo in https://github.com/PennLINC/xcpd/pull/1061 ### Other Changes
Add information about ReHo to read-the-docs by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/1097
Update landing page figure by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/1099
Add band over censored volumes in executive summary carpet plots by @tsalo in https://github.com/PennLINC/xcp_d/pull/1077

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.6.4...0.7.0rc1

- Python
Published by tsalo almost 2 years ago

xcp_d - 0.6.4

What's Changed

🎉 Exciting New Features

Replace bids:xcp_d: BIDS URI with bids:: by @tsalo in https://github.com/PennLINC/xcp_d/pull/1088 ### 👎 Deprecations
[DCAN] Enable DCAN QC by default by @tsalo in https://github.com/PennLINC/xcp_d/pull/1086 ### 🐛 Bug Fixes
Raise error if atlas affines don't match across participants by @tsalo in https://github.com/PennLINC/xcp_d/pull/1075
Fix query error report in collect_mesh_data by @tsalo in https://github.com/PennLINC/xcp_d/pull/1092
Adopt Lindquist-compliant denoising method by @tsalo in https://github.com/PennLINC/xcp_d/pull/1087 ### Other Changes
Update changelog for 0.6.3 by @tsalo in https://github.com/PennLINC/xcp_d/pull/1079

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.6.3...0.6.4

- Python
Published by tsalo almost 2 years ago

xcp_d - 0.6.3

What's Changed

🎉 Exciting New Features

Make "DatasetType" key recommended, not required by @tsalo in https://github.com/PennLINC/xcp_d/pull/1068 ### 🐛 Bug Fixes
Do not warn if fd-thresh and min-time are both set to 0 by @tsalo in https://github.com/PennLINC/xcp_d/pull/1071
Use copy_atlas to write out atlas tsv and json files by @tsalo in https://github.com/PennLINC/xcp_d/pull/1073
Raise error if FSLICENSE environment variable is not an existing file by @tsalo in https://github.com/PennLINC/xcpd/pull/1072
Generate T2w executive summary plots when T1w is also available by @tsalo in https://github.com/PennLINC/xcp_d/pull/1078 ### Other Changes
Add release notes for releases 0.6.1 and 0.6.2 by @tsalo in https://github.com/PennLINC/xcp_d/pull/1070

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.6.2...0.6.3

- Python
Published by tsalo almost 2 years ago

xcp_d - 0.6.2

What's Changed

🐛 Bug Fixes

Raise interpretable error when no BOLD runs survive minimum-time threshold by @tsalo in https://github.com/PennLINC/xcp_d/pull/1048
Address bug with T2w-only processing by @tsalo in https://github.com/PennLINC/xcp_d/pull/1060
Use strict file-matching in collectrundata by @tsalo in https://github.com/PennLINC/xcp_d/pull/1063
Fix potential atlas file race condition by @tsalo in https://github.com/PennLINC/xcp_d/pull/1066 ### Other Changes
Make description of smoothing parameter clearer when set to 0 by @psychelzh in https://github.com/PennLINC/xcp_d/pull/1056

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.6.1...0.6.2

- Python
Published by tsalo almost 2 years ago

xcp_d - 0.6.1

What's Changed

🛠 Breaking Changes

Support ALFF for censored data by @tsalo in https://github.com/PennLINC/xcp_d/pull/1020
Move atlases into a subfolder by @tsalo in https://github.com/PennLINC/xcp_d/pull/1024 ### 🎉 Exciting New Features
Add colorbar to ALFF and ReHo plots by @tsalo in https://github.com/PennLINC/xcp_d/pull/1023
Add options for UK Biobank data by @tsalo in https://github.com/PennLINC/xcp_d/pull/1022
Add options to subset atlases by @tsalo in https://github.com/PennLINC/xcp_d/pull/1034
Support MCRIBS derivatives by @tsalo in https://github.com/PennLINC/xcp_d/pull/1029
Add --stop-on-first-crash option to command-line interface by @tsalo in https://github.com/PennLINC/xcp_d/pull/1044 ### 🐛 Bug Fixes
Rescale ALFF based on original BOLD standard deviation by @tsalo in https://github.com/PennLINC/xcp_d/pull/1033
Drop dir entity from concatenated filenames by @tsalo in https://github.com/PennLINC/xcp_d/pull/1037
Fix dscalar CIFTI generation by @tsalo in https://github.com/PennLINC/xcp_d/pull/1036
Fix TR in denoised NIfTI headers by @tsalo in https://github.com/PennLINC/xcp_d/pull/1038 ### Other Changes
Add dependabot Action by @tsalo in https://github.com/PennLINC/xcp_d/pull/1006
Update to Python 3.10 by @tsalo in https://github.com/PennLINC/xcp_d/pull/1016
Update docker image link by @psychelzh in https://github.com/PennLINC/xcp_d/pull/1045

New Contributors

@dependabot made their first contribution in https://github.com/PennLINC/xcp_d/pull/1007
@psychelzh made their first contribution in https://github.com/PennLINC/xcp_d/pull/1045

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.6.0...0.6.1

- Python
Published by tsalo about 2 years ago

xcp_d - 0.6.1rc1

This release adds support for UK Biobank preprocessing derivatives, for the NiCharts project.

What's Changed

🛠 Breaking Changes

Support ALFF for censored data by @tsalo in https://github.com/PennLINC/xcp_d/pull/1020
Move atlases into a subfolder by @tsalo in https://github.com/PennLINC/xcp_d/pull/1024

🎉 Exciting New Features

Add colorbar to ALFF and ReHo plots by @tsalo in https://github.com/PennLINC/xcp_d/pull/1023
Add options for UK Biobank data by @tsalo in https://github.com/PennLINC/xcp_d/pull/1022

🐛 Bug Fixes

Rescale ALFF based on original BOLD standard deviation by @tsalo in https://github.com/PennLINC/xcp_d/pull/1033

Other Changes

Add dependabot Action by @tsalo in https://github.com/PennLINC/xcp_d/pull/1006
Update to Python 3.10 by @tsalo in https://github.com/PennLINC/xcp_d/pull/1016

New Contributors

@dependabot made their first contribution in https://github.com/PennLINC/xcp_d/pull/1007

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.6.0...0.6.1rc1

- Python
Published by tsalo about 2 years ago

xcp_d - 0.6.0

What's Changed

🛠 Breaking Changes

Replace Schaefer atlases with AtlasPack by @tsalo in https://github.com/PennLINC/xcp_d/pull/928
Update the QC metrics by @tsalo in https://github.com/PennLINC/xcp_d/pull/958
Track Sources for outputs with BIDS URIs by @tsalo in https://github.com/PennLINC/xcp_d/pull/966
Replace AtlasPack 0.0.5 atlases with AtlasPack 0.1.0 atlases by @tsalo in https://github.com/PennLINC/xcp_d/pull/991 ### 🎉 Exciting New Features
Split HCP tasks into task and run entities by @tsalo in https://github.com/PennLINC/xcp_d/pull/952
Concatenate across directions as well as runs by @tsalo in https://github.com/PennLINC/xcp_d/pull/965
Retain orthogonalized confounds by @tsalo in https://github.com/PennLINC/xcp_d/pull/975
Improve connectivity plots by @tsalo in https://github.com/PennLINC/xcp_d/pull/988
Produce correlation matrices for concatenated time series by @tsalo in https://github.com/PennLINC/xcp_d/pull/990 ### 🐛 Bug Fixes
Fix resting-state plots in executive summary by @tsalo in https://github.com/PennLINC/xcp_d/pull/941
Load T1w-to-standard transform to same space as volumetric BOLD scan by @tsalo in https://github.com/PennLINC/xcp_d/pull/926
Pin Nilearn version by @tsalo in https://github.com/PennLINC/xcp_d/pull/955
Don't interpolate volumes at beginning/end of run by @tsalo in https://github.com/PennLINC/xcp_d/pull/950
Look for flirtbbr figure by @tsalo in https://github.com/PennLINC/xcp_d/pull/980
Make registration figure in executive summary optional by @tsalo in https://github.com/PennLINC/xcp_d/pull/981
Don't convert CIFTIs to int16 by @tsalo in https://github.com/PennLINC/xcp_d/pull/979
Store temporary files in working directory by @tsalo in https://github.com/PennLINC/xcp_d/pull/985
Fix HCP ingression for non-rest tasks by @tsalo in https://github.com/PennLINC/xcp_d/pull/986
Allow executive summary registration figure to really be empty by @tsalo in https://github.com/PennLINC/xcp_d/pull/987
Allow motion filtering when motion-based censoring is disabled by @tsalo in https://github.com/PennLINC/xcp_d/pull/994
Fix node labels and communities in Gordon atlas by @tsalo in https://github.com/PennLINC/xcp_d/pull/996
Fix coverage CIFTIs by @tsalo in https://github.com/PennLINC/xcp_d/pull/998
Remove unused native-space support by @tsalo in https://github.com/PennLINC/xcp_d/pull/1003 ### Other Changes
Update documentation for 0.5.0 release by @tsalo in https://github.com/PennLINC/xcp_d/pull/937
Try to reduce memory requirements of functional connectivity nodes by @tsalo in https://github.com/PennLINC/xcp_d/pull/982
Try to reduce memory requirements of denoising node by @tsalo in https://github.com/PennLINC/xcp_d/pull/989
Prepare for 0.6.0 by @tsalo in https://github.com/PennLINC/xcp_d/pull/1005

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.5.0...0.6.0

- Python
Published by tsalo about 2 years ago

xcp_d - 0.6.0rc6

What's Changed

🛠 Breaking Changes

Replace AtlasPack 0.0.5 atlases with AtlasPack 0.1.0 atlases by @tsalo in https://github.com/PennLINC/xcp_d/pull/991 ### 🎉 Exciting New Features
Improve connectivity plots by @tsalo in https://github.com/PennLINC/xcp_d/pull/988
Produce correlation matrices for concatenated time series by @tsalo in https://github.com/PennLINC/xcp_d/pull/990 ### 🐛 Bug Fixes
Allow motion filtering when motion-based censoring is disabled by @tsalo in https://github.com/PennLINC/xcp_d/pull/994
Fix node labels and communities in Gordon atlas by @tsalo in https://github.com/PennLINC/xcp_d/pull/996 ### Other Changes
Try to reduce memory requirements of denoising node by @tsalo in https://github.com/PennLINC/xcp_d/pull/989

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.6.0rc5...0.6.0rc6

- Python
Published by tsalo over 2 years ago

xcp_d - 0.6.0rc5

What's Changed

🐛 Bug Fixes

Allow executive summary registration figure to really be empty by @tsalo in https://github.com/PennLINC/xcp_d/pull/987

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.6.0rc4...0.6.0rc5

- Python
Published by tsalo over 2 years ago

xcp_d - 0.6.0rc4

What's Changed

🐛 Bug Fixes

Fix HCP ingression for non-rest tasks by @tsalo in https://github.com/PennLINC/xcp_d/pull/986

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.6.0rc3...0.6.0rc4

- Python
Published by tsalo over 2 years ago

xcp_d - 0.6.0rc3

What's Changed

🐛 Bug Fixes

Don't convert CIFTIs to int16 by @tsalo in https://github.com/PennLINC/xcp_d/pull/979
Store temporary files in working directory by @tsalo in https://github.com/PennLINC/xcp_d/pull/985 ### Other Changes
Try to reduce memory requirements of functional connectivity nodes by @tsalo in https://github.com/PennLINC/xcp_d/pull/982

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.6.0rc2...0.6.0rc3

- Python
Published by tsalo over 2 years ago

xcp_d - 0.6.0rc2

What's Changed

🐛 Bug Fixes

Make registration figure in executive summary optional by @tsalo in https://github.com/PennLINC/xcp_d/pull/981

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.6.0rc1...0.6.0rc2

- Python
Published by tsalo over 2 years ago

xcp_d - 0.6.0rc1

What's Changed

🛠 Breaking Changes

Replace Schaefer atlases with AtlasPack by @tsalo in https://github.com/PennLINC/xcp_d/pull/928
Update the QC metrics by @tsalo in https://github.com/PennLINC/xcp_d/pull/958
Track Sources for outputs with BIDS URIs by @tsalo in https://github.com/PennLINC/xcp_d/pull/966 ### 🎉 Exciting New Features
Split HCP tasks into task and run entities by @tsalo in https://github.com/PennLINC/xcp_d/pull/952
Concatenate across directions as well as runs by @tsalo in https://github.com/PennLINC/xcp_d/pull/965
Retain orthogonalized confounds by @tsalo in https://github.com/PennLINC/xcp_d/pull/975 ### 🐛 Bug Fixes
Fix resting-state plots in executive summary by @tsalo in https://github.com/PennLINC/xcp_d/pull/941
Load T1w-to-standard transform to same space as volumetric BOLD scan by @tsalo in https://github.com/PennLINC/xcp_d/pull/926
Pin Nilearn version by @tsalo in https://github.com/PennLINC/xcp_d/pull/955
Don't interpolate volumes at beginning/end of run by @tsalo in https://github.com/PennLINC/xcp_d/pull/950
Look for flirtbbr figure by @tsalo in https://github.com/PennLINC/xcp_d/pull/980 ### Other Changes
Update documentation for 0.5.0 release by @tsalo in https://github.com/PennLINC/xcp_d/pull/937

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.5.0...0.6.0rc1

- Python
Published by tsalo over 2 years ago

xcp_d - 0.5.2

What's Changed

Other Changes

Fix HCP ingression for non-rest tasks. by @tsalo in https://github.com/PennLINC/xcp_d/pull/972

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.5.1...0.5.2

- Python
Published by tsalo over 2 years ago

xcp_d - 0.5.1

What's Changed

Other Changes

Update documentation for 0.5.0 release by @tsalo in https://github.com/PennLINC/xcp_d/pull/937
Reproduce recent changes for 0.5.1 by @tsalo in https://github.com/PennLINC/xcp_d/pull/964
Update docs for 0.5.1 by @tsalo in https://github.com/PennLINC/xcp_d/pull/969

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.5.0...0.5.1

- Python
Published by tsalo over 2 years ago

xcp_d - 0.5.0

The 0.5.0 release prepares for the XCP-D manuscript, so I plan to not introduce any backwards-incompatible changes between this release and 1.0.0 (the official paper release).

What's Changed

🛠 Breaking Changes

Add CIFTI subcortical atlas to XCP-D by @tsalo in https://github.com/PennLINC/xcp_d/pull/864
Change "ciftiSubcortical" atlas name to "HCP" by @tsalo in https://github.com/PennLINC/xcp_d/pull/932 ### 🎉 Exciting New Features
Write out top-level sidecar for PennLINC QC file by @tsalo in https://github.com/PennLINC/xcp_d/pull/894
Parcellate ReHo, ALFF, and surface morphometric maps by @tsalo in https://github.com/PennLINC/xcp_d/pull/839
Refactor dcan/hcp ingestion and add more surface files by @tsalo in https://github.com/PennLINC/xcp_d/pull/887
Add "none" option for denoising by @tsalo in https://github.com/PennLINC/xcp_d/pull/879
Add --exact-time parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/885
Allow white matter surface suffix to be either "smoothwm" or "white" by @tsalo in https://github.com/PennLINC/xcp_d/pull/899
Add --fs-license-file parameter to command line interface by @tsalo in https://github.com/PennLINC/xcp_d/pull/930
Generate executive summary figures without --dcan-qc by @tsalo in https://github.com/PennLINC/xcp_d/pull/936 ### 🐛 Bug Fixes
Standardize executive summary carpet if params is "none" by @tsalo in https://github.com/PennLINC/xcp_d/pull/916
Support CIFTI morphometry files and add PNC test data by @tsalo in https://github.com/PennLINC/xcp_d/pull/922
Correct ABCD/HCP surface ingression by @tsalo in https://github.com/PennLINC/xcp_d/pull/927 ### Other Changes
Add contributing documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/893
Update changelog and CFF file for 0.4.0 by @tsalo in https://github.com/PennLINC/xcp_d/pull/896
Change packaging to use hatch-vcs and pyproject.toml by @tsalo in https://github.com/PennLINC/xcp_d/pull/897
Fix description of signal denoising method in docs by @tsalo in https://github.com/PennLINC/xcp_d/pull/898
Improve QC sidecar contents by @tsalo in https://github.com/PennLINC/xcp_d/pull/900
Rename the parcellated ALFF/ReHo outputs by @tsalo in https://github.com/PennLINC/xcp_d/pull/902
Remove workaround for nonbinary Nibabies brain masks by @tsalo in https://github.com/PennLINC/xcp_d/pull/905
Update Landing Page Figure by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/908
Remove unused functions in filemanip module by @tsalo in https://github.com/PennLINC/xcp_d/pull/911
Add tests for xcpd.utils.utils module by @tsalo in https://github.com/PennLINC/xcpd/pull/910
Add tests for xcpd.utils.execsummary module by @tsalo in https://github.com/PennLINC/xcpd/pull/912
Expand tests by @tsalo in https://github.com/PennLINC/xcp_d/pull/913
Test CLI parameter validation by @tsalo in https://github.com/PennLINC/xcp_d/pull/918
Refactor collection functions by @tsalo in https://github.com/PennLINC/xcp_d/pull/917

Full Changelog: https://github.com/PennLINC/xcp_d/compare/04.0...0.5.0

- Python
Published by tsalo over 2 years ago

xcp_d - 0.5.0rc2

This fixes the atlas name for the CIFTI subcortical atlas.

What's Changed

🛠 Breaking Changes

Change "ciftiSubcortical" atlas name to "HCP" by @tsalo in https://github.com/PennLINC/xcp_d/pull/932

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.5.0rc1...0.5.0rc2

- Python
Published by tsalo over 2 years ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/864 ### 🎉 Exciting New Features
Refactor dcan/hcp ingestion and add more surface files by @tsalo in https://github.com/PennLINC/xcp_d/pull/887
Add "none" option for denoising by @tsalo in https://github.com/PennLINC/xcp_d/pull/879
Add --exact-time parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/885
Allow white matter surface suffix to be either "smoothwm" or "white" by @tsalo in https://github.com/PennLINC/xcp_d/pull/899
Add --fs-license-file parameter to command line interface by @tsalo in https://github.com/PennLINC/xcp_d/pull/930 ### 🐛 Bug Fixes
Standardize executive summary carpet if params is "none" by @tsalo in https://github.com/PennLINC/xcp_d/pull/916
Support CIFTI morphometry files and add PNC test data by @tsalo in https://github.com/PennLINC/xcp_d/pull/922
Correct ABCD/HCP surface ingression by @tsalo in https://github.com/PennLINC/xcp_d/pull/927 ### Other Changes
Improve QC sidecar contents by @tsalo in https://github.com/PennLINC/xcp_d/pull/900
Rename the parcellated ALFF/ReHo outputs by @tsalo in https://github.com/PennLINC/xcp_d/pull/902
Remove workaround for nonbinary Nibabies brain masks by @tsalo in https://github.com/PennLINC/xcp_d/pull/905
Update Landing Page Figure by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/908
Remove unused functions in filemanip module by @tsalo in https://github.com/PennLINC/xcp_d/pull/911
Add tests for xcpd.utils.utils module by @tsalo in https://github.com/PennLINC/xcpd/pull/910
Add tests for xcpd.utils.execsummary module by @tsalo in https://github.com/PennLINC/xcpd/pull/912
Expand tests by @tsalo in https://github.com/PennLINC/xcp_d/pull/913
Test CLI parameter validation by @tsalo in https://github.com/PennLINC/xcp_d/pull/918
Refactor collection functions by @tsalo in https://github.com/PennLINC/xcp_d/pull/917

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.4.1rc2...0.5.0rc1

- Python
Published by tsalo over 2 years ago

xcp_d - 0.4.1rc2

What's Changed

Other Changes

Fix description of signal denoising method in docs by @tsalo in https://github.com/PennLINC/xcp_d/pull/898

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.4.1rc1...0.4.1rc2

- Python
Published by tsalo over 2 years ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/894
Parcellate ReHo, ALFF, and surface morphometric maps by @tsalo in https://github.com/PennLINC/xcp_d/pull/839 ### Other Changes
Add contributing documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/893
Update changelog and CFF file for 0.4.0 by @tsalo in https://github.com/PennLINC/xcp_d/pull/896
Change packaging to use hatch-vcs and pyproject.toml by @tsalo in https://github.com/PennLINC/xcp_d/pull/897

Full Changelog: https://github.com/PennLINC/xcp_d/compare/04.0...0.4.1rc1

- Python
Published by tsalo over 2 years ago

xcp_d - 0.4.0

What's Changed

🛠 Breaking Changes

Change default highpass filter cutoff from 0.009 to 0.01 by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/755
Refactor anatomical workflow by @tsalo in https://github.com/PennLINC/xcp_d/pull/706
Do not require --combineruns to generate DCAN QC files by @tsalo in https://github.com/PennLINC/xcp_d/pull/753
Change QC filenames and fix xcp_d-combineqc command-line interface by @tsalo in https://github.com/PennLINC/xcp_d/pull/762
Retain cohort entity in derivative filenames by @tsalo in https://github.com/PennLINC/xcp_d/pull/769
Require the --cifti flag in order to use --warp-surfaces-native2std by @tsalo in https://github.com/PennLINC/xcp_d/pull/770
Zero out parcels with <50% coverage by @tsalo in https://github.com/PennLINC/xcp_d/pull/757
Use constant padding and maximum padlen for temporal filtering by @tsalo in https://github.com/PennLINC/xcp_d/pull/779
Replace non-aggressive denoising with orthogonalization and streamline denoising by @tsalo in https://github.com/PennLINC/xcp_d/pull/808
Add design matrix to report by @tsalo in https://github.com/PennLINC/xcp_d/pull/824
Write out censored results by @tsalo in https://github.com/PennLINC/xcp_d/pull/820
Allow users to disable censoring, and only generate ALFF if censoring is disabled by @tsalo in https://github.com/PennLINC/xcp_d/pull/828
Implement --min-time parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/836
Remove deprecated --dummytime parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/837
Change FD Threshold from 0.2 to 0.3 by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/854
Use filtered motion in nuisance regression by @tsalo in https://github.com/PennLINC/xcp_d/pull/871 ### 🎉 Exciting New Features
Add option to estimate brain radius from brain mask by @tsalo in https://github.com/PennLINC/xcp_d/pull/754
Output warped atlases to derivatives by @tsalo in https://github.com/PennLINC/xcp_d/pull/647
Add min_coverage parameter to threshold parcel coverage by @tsalo in https://github.com/PennLINC/xcp_d/pull/782
Improve executive summary carpet plots by @tsalo in https://github.com/PennLINC/xcp_d/pull/747
Output T2w images if available by @tsalo in https://github.com/PennLINC/xcp_d/pull/648
Generate CIFTI and TSV versions of coverage, timeseries, and correlation files by @tsalo in https://github.com/PennLINC/xcp_d/pull/785
Add colorbar to executive summary carpet plots by @tsalo in https://github.com/PennLINC/xcp_d/pull/829
Support fsLR-space shape files generated by preprocessing pipelines by @tsalo in https://github.com/PennLINC/xcp_d/pull/773
Support preprocessing derivatives with T2w, but no T1w by @tsalo in https://github.com/PennLINC/xcp_d/pull/838
Support high-pass or low-pass only filtering by @smeisler in https://github.com/PennLINC/xcp_d/pull/862 ### 🐛 Bug Fixes
Replace missing vertices' values with NaNs by @tsalo in https://github.com/PennLINC/xcp_d/pull/743
Select MNI152NLin6Asym target space for T1w from CIFTI derivatives by @tsalo in https://github.com/PennLINC/xcp_d/pull/759
Only generate brainsprite figures when the --dcan_qc flag is used by @tsalo in https://github.com/PennLINC/xcp_d/pull/766
Check for existence of datasetdescription.json in fmridir by @tsalo in https://github.com/PennLINC/xcp_d/pull/806
Move dataset desc check to after conversion by @tsalo in https://github.com/PennLINC/xcp_d/pull/809
Refactor HCP/DCAN ingression and fix converted filenames by @tsalo in https://github.com/PennLINC/xcp_d/pull/714
Connect custom confounds to confound consolidation node by @tsalo in https://github.com/PennLINC/xcp_d/pull/835
Work around loadconfounds aCompCor bug by @tsalo in https://github.com/PennLINC/xcpd/pull/851
Allow for smoothing to be zero by @tsalo in https://github.com/PennLINC/xcp_d/pull/861
Use appropriate T1w/T2w in brainsprite workflow by @tsalo in https://github.com/PennLINC/xcp_d/pull/860
Test DCAN and HCP ingestion and fix related bugs by @tsalo in https://github.com/PennLINC/xcp_d/pull/848 ### Other Changes
Add tests for cifti smoothness by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/659
Fix CIFTI downcasting test by @tsalo in https://github.com/PennLINC/xcp_d/pull/752
Use pytest to test command-line interface by @tsalo in https://github.com/PennLINC/xcp_d/pull/740
Upload coverage reports to CodeCov by @tsalo in https://github.com/PennLINC/xcp_d/pull/758
Link to xcp_d-examples in documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/761
Add information about preprocessing requirements by @tsalo in https://github.com/PennLINC/xcp_d/pull/772
Replace MultiLabel interpolation with GenericLabel by @tsalo in https://github.com/PennLINC/xcp_d/pull/786
Mention cosine regressors in aCompCor boilerplate by @tsalo in https://github.com/PennLINC/xcp_d/pull/788
Update base Docker image by @tsalo in https://github.com/PennLINC/xcp_d/pull/799
Document Singularity requirements by @tsalo in https://github.com/PennLINC/xcp_d/pull/805
Use workflow nodes for workflow tests by @tsalo in https://github.com/PennLINC/xcp_d/pull/807
Adjust code for niworkflows 1.7.3 by @tsalo in https://github.com/PennLINC/xcp_d/pull/810
Use a workflow for concatenation by @tsalo in https://github.com/PennLINC/xcp_d/pull/821
Create prepareconfounds and denoisebold workflows by @tsalo in https://github.com/PennLINC/xcp_d/pull/827
Simplify the anatomical workflow some more by @tsalo in https://github.com/PennLINC/xcp_d/pull/841
Remove codecov dependency by @tsalo in https://github.com/PennLINC/xcp_d/pull/850
Add boilerplate to the executive summary by @tsalo in https://github.com/PennLINC/xcp_d/pull/857
Add additional argument aliases by @smeisler in https://github.com/PennLINC/xcp_d/pull/870
Update docs to mention HCPYA version by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/869
Improve boilerplate by @tsalo in https://github.com/PennLINC/xcp_d/pull/866
Update gitignore by @tsalo in https://github.com/PennLINC/xcp_d/pull/874
Fix issues with HCP Ingression by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/872
Document how to process multiple, but not all, tasks by @tsalo in https://github.com/PennLINC/xcp_d/pull/876
Describe scope of XCP-D by @tsalo in https://github.com/PennLINC/xcp_d/pull/878
Update docs by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/882
Always generate the DCAN executive summary by @tsalo in https://github.com/PennLINC/xcp_d/pull/888
Clean up testing framework and documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/889

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.3.2...04.0

- Python
Published by tsalo over 2 years ago

xcp_d - 0.4.0rc2

What's Changed

🛠 Breaking Changes

Replace non-aggressive denoising with orthogonalization and steamline denoising by @tsalo in https://github.com/PennLINC/xcp_d/pull/808
Add design matrix to report by @tsalo in https://github.com/PennLINC/xcp_d/pull/824
Write out censored results by @tsalo in https://github.com/PennLINC/xcp_d/pull/820
Allow users to disable censoring, and only generate ALFF if censoring is disabled by @tsalo in https://github.com/PennLINC/xcp_d/pull/828 ### 🎉 Exciting New Features
Generate CIFTI and TSV versions of coverage, timeseries, and correlation files by @tsalo in https://github.com/PennLINC/xcp_d/pull/785 ### 🐛 Bug Fixes
Check for existence of datasetdescription.json in fmridir by @tsalo in https://github.com/PennLINC/xcp_d/pull/806
Move dataset desc check to after conversion by @tsalo in https://github.com/PennLINC/xcp_d/pull/809
Refactor HCP/DCAN ingression and fix converted filenames by @tsalo in https://github.com/PennLINC/xcp_d/pull/714 ### Other Changes
Document Singularity requirements by @tsalo in https://github.com/PennLINC/xcp_d/pull/805
Use workflow nodes for workflow tests by @tsalo in https://github.com/PennLINC/xcp_d/pull/807
Adjust code for niworkflows 1.7.3 by @tsalo in https://github.com/PennLINC/xcp_d/pull/810
Use a workflow for concatenation by @tsalo in https://github.com/PennLINC/xcp_d/pull/821
Create prepareconfounds and denoisebold workflows by @tsalo in https://github.com/PennLINC/xcp_d/pull/827

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.4.0rc1...0.4.0rc2

- Python
Published by tsalo almost 3 years ago

xcp_d - 0.4.0rc1

What's Changed

🛠 Breaking Changes

Change default highpass filter cutoff from 0.009 to 0.01 by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/755
Refactor anatomical workflow by @tsalo in https://github.com/PennLINC/xcp_d/pull/706
Do not require --combineruns to generate DCAN QC files by @tsalo in https://github.com/PennLINC/xcp_d/pull/753
Change QC filenames and fix xcp_d-combineqc command-line interface by @tsalo in https://github.com/PennLINC/xcp_d/pull/762
Retain cohort entity in derivative filenames by @tsalo in https://github.com/PennLINC/xcp_d/pull/769
Require the --cifti flag in order to use --warp-surfaces-native2std by @tsalo in https://github.com/PennLINC/xcp_d/pull/770
Zero out parcels with <50% coverage by @tsalo in https://github.com/PennLINC/xcp_d/pull/757
Use constant padding and maximum padlen for temporal filtering by @tsalo in https://github.com/PennLINC/xcp_d/pull/779 ### 🎉 Exciting New Features
Add option to estimate brain radius from brain mask by @tsalo in https://github.com/PennLINC/xcp_d/pull/754
Output warped atlases to derivatives by @tsalo in https://github.com/PennLINC/xcp_d/pull/647
Add min_coverage parameter to threshold parcel coverage by @tsalo in https://github.com/PennLINC/xcp_d/pull/782
Improve executive summary carpet plots by @tsalo in https://github.com/PennLINC/xcp_d/pull/747
Output T2w images if available by @tsalo in https://github.com/PennLINC/xcp_d/pull/648 ### 🐛 Bug Fixes
Replace missing vertices' values with NaNs by @tsalo in https://github.com/PennLINC/xcp_d/pull/743
Select MNI152NLin6Asym target space for T1w from CIFTI derivatives by @tsalo in https://github.com/PennLINC/xcp_d/pull/759
Only generate brainsprite figures when the --dcan_qc flag is used by @tsalo in https://github.com/PennLINC/xcp_d/pull/766 ### Other Changes
Add tests for cifti smoothness by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/659
Fix CIFTI downcasting test by @tsalo in https://github.com/PennLINC/xcp_d/pull/752
Use pytest to test command-line interface by @tsalo in https://github.com/PennLINC/xcp_d/pull/740
Upload coverage reports to CodeCov by @tsalo in https://github.com/PennLINC/xcp_d/pull/758
Link to xcp_d-examples in documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/761
Add information about preprocessing requirements by @tsalo in https://github.com/PennLINC/xcp_d/pull/772
Replace MultiLabel interpolation with GenericLabel by @tsalo in https://github.com/PennLINC/xcp_d/pull/786
Mention cosine regressors in aCompCor boilerplate by @tsalo in https://github.com/PennLINC/xcp_d/pull/788
Update base Docker image by @tsalo in https://github.com/PennLINC/xcp_d/pull/799

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.3.2...0.4.0rc1

- Python
Published by tsalo about 3 years ago

xcp_d - 0.3.3rc4

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.3.3rc3...0.3.3rc4

- Python
Published by tsalo about 3 years ago

xcp_d - 0.3.3rc3

What's Changed

Other Changes

MAINT 0.3.x: Update base Docker image by @tsalo in https://github.com/PennLINC/xcp_d/pull/798

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.3.3rc2...0.3.3rc3

- Python
Published by tsalo about 3 years ago

xcp_d - 0.3.3rc2

What's Changed

Other Changes

Update Dockerfile by @tsalo in https://github.com/PennLINC/xcp_d/pull/797

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.3.3rc1...0.3.3rc2

- Python
Published by tsalo about 3 years ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/795

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.3.2...0.3.3rc1

- Python
Published by tsalo about 3 years ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/702 ### Other Changes
Remove example data and fix workflow graphs by @tsalo in https://github.com/PennLINC/xcp_d/pull/738
Replace CiftiDespike with connected nodes by @tsalo in https://github.com/PennLINC/xcp_d/pull/737

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.3.1...0.3.2

- Python
Published by tsalo about 3 years ago

xcp_d - 0.3.1

What's Changed

🛠 Breaking Changes

Remove --nuissance-regressors and --bandpass_filter by @tsalo in https://github.com/PennLINC/xcp_d/pull/658 ### 🎉 Exciting New Features
Add --dummy-scans parameter and deprecate --dummytime by @tsalo in https://github.com/PennLINC/xcp_d/pull/616
Add --bids-filter-file parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/686
Enable non-aggressive denoising with signal regressors by @tsalo in https://github.com/PennLINC/xcp_d/pull/697
Improve identification of FreeSurfer derivatives by @tsalo in https://github.com/PennLINC/xcp_d/pull/719
Collect preprocessed surfaces in new function by @tsalo in https://github.com/PennLINC/xcp_d/pull/731 ### 🐛 Bug Fixes
Remove dummy volumes from custom confounds files by @tsalo in https://github.com/PennLINC/xcp_d/pull/660
Remove dummy volumes from beginning of each run in concatenation workflow by @tsalo in https://github.com/PennLINC/xcp_d/pull/661
Retain noise components instead of dropping them in loadaroma by @tsalo in https://github.com/PennLINC/xcpd/pull/670
Use inputtype to determine order of preferred spaces by @tsalo in https://github.com/PennLINC/xcpd/pull/688
Infer volumetric space from transform in executive summary with cifti data by @tsalo in https://github.com/PennLINC/xcp_d/pull/689
Change input type from HPC to HCP by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/691
Replace failing non-aggressive AROMA denoising with working aggressive denoising by @tsalo in https://github.com/PennLINC/xcp_d/pull/693
Select best volumetric space for transforms even when using --cifti flag by @tsalo in https://github.com/PennLINC/xcp_d/pull/695
Downcast >32-bit files to 32-bit by @tsalo in https://github.com/PennLINC/xcp_d/pull/666
Use appropriate intent codes for cifti outputs by @tsalo in https://github.com/PennLINC/xcp_d/pull/690
Only concatenate processed runs by @tsalo in https://github.com/PennLINC/xcp_d/pull/713
Do not use downcasted files as name sources by @tsalo in https://github.com/PennLINC/xcp_d/pull/712
Warp segmentation file to appropriate space for carpet plots by @tsalo in https://github.com/PennLINC/xcp_d/pull/727
Use brain mask in NIFTI connectivity workflow by @tsalo in https://github.com/PennLINC/xcp_d/pull/733 ### Other Changes
Consolidate confounds at beginning of denoising workflows by @tsalo in https://github.com/PennLINC/xcp_d/pull/664
Remove unused outputnodes from nifti and cifti workflows by @tsalo in https://github.com/PennLINC/xcp_d/pull/667
Move QC/censoring plots into new workflow by @tsalo in https://github.com/PennLINC/xcp_d/pull/668
Testing affines don't change across XCP runs by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/649
Load confounds via Nilearn functionality by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/675
Update docs by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/682
Add masks to package data by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/715
Use ds001491 fMRIPrep derivatives for tests by @tsalo in https://github.com/PennLINC/xcp_d/pull/698
Add tests for confound loading function by @tsalo in https://github.com/PennLINC/xcp_d/pull/730
Refactor executive summary workflow by @tsalo in https://github.com/PennLINC/xcp_d/pull/721
Track start of workflow with sentry by @tsalo in https://github.com/PennLINC/xcp_d/pull/732

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.3.0...0.3.1

- Python
Published by tsalo about 3 years ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/601
Add --dcan-qc flag by @tsalo in https://github.com/PennLINC/xcp_d/pull/650
Support custom confounds with headers by @tsalo in https://github.com/PennLINC/xcp_d/pull/642 ### 🎉 Exciting New Features
Use BIDSLayout in concatenation code by @tsalo in https://github.com/PennLINC/xcp_d/pull/600
[ENH] Support Nibabies ingression into XCP by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/602
Add static ALFF and ReHo plots to report by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/604
Write confounds out to derivatives by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/634
Add column names to confounds df by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/641 ### 🐛 Bug Fixes
Select BOLD files in a single space by @tsalo in https://github.com/PennLINC/xcp_d/pull/603
Censor data in executive summary plots correctly by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/614
Only generate ALFF derivatives if bandpass filtering is enabled by @tsalo in https://github.com/PennLINC/xcp_d/pull/628
Do not merge in concatenated files when re-running concatenation workflow by @tsalo in https://github.com/PennLINC/xcp_d/pull/633
Map abbreviated entities to full names for templateflow get call by @tsalo in https://github.com/PennLINC/xcp_d/pull/654
Ensure dummyscans is an integer in PlotSVGData by @tsalo in https://github.com/PennLINC/xcp_d/pull/655 ### Other Changes
Use Nilearn for brainsprite generation by @tsalo in https://github.com/PennLINC/xcp_d/pull/607
Cache the downloaded test data by @tsalo in https://github.com/PennLINC/xcp_d/pull/629
Use BIDSLayout instead of globbing functions to collect necessary files by @tsalo in https://github.com/PennLINC/xcp_d/pull/621
Start to standardize interface parameter calls by @tsalo in https://github.com/PennLINC/xcp_d/pull/638
Simplify transform-getting functions by @tsalo in https://github.com/PennLINC/xcp_d/pull/623
Lint with black without linting workflow connections by @tsalo in https://github.com/PennLINC/xcp_d/pull/640

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.2.0...0.3.0

- Python
Published by tsalo over 3 years ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/634
Add column names to confounds df by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/641 ### 🐛 Bug Fixes
Do not merge in concatenated files when re-running concatenation workflow by @tsalo in https://github.com/PennLINC/xcp_d/pull/633
Map abbreviated entities to full names for templateflow get call by @tsalo in https://github.com/PennLINC/xcp_d/pull/654
Ensure dummyscans is an integer in PlotSVGData by @tsalo in https://github.com/PennLINC/xcp_d/pull/655 ### Other Changes
Cache the downloaded test data by @tsalo in https://github.com/PennLINC/xcp_d/pull/629
Use BIDSLayout instead of globbing functions to collect necessary files by @tsalo in https://github.com/PennLINC/xcp_d/pull/621
Start to standardize interface parameter calls by @tsalo in https://github.com/PennLINC/xcp_d/pull/638
Simplify transform-getting functions by @tsalo in https://github.com/PennLINC/xcp_d/pull/623
Lint with black without linting workflow connections by @tsalo in https://github.com/PennLINC/xcp_d/pull/640

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.2.1...0.2.2

- Python
Published by tsalo over 3 years ago

xcp_d - 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 https://github.com/PennLINC/xcp_d/pull/601 ### 🎉 Exciting New Features
Use BIDSLayout in concatenation code by @tsalo in https://github.com/PennLINC/xcp_d/pull/600
[ENH] Support Nibabies ingression into XCP by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/602
Add static ALFF and ReHo plots to report by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/604 ### 🐛 Bug Fixes
Select BOLD files in a single space by @tsalo in https://github.com/PennLINC/xcp_d/pull/603
Censor data in executive summary plots correctly by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/614
Only generate ALFF derivatives if bandpass filtering is enabled by @tsalo in https://github.com/PennLINC/xcp_d/pull/628 ### Other Changes
Use Nilearn for brainsprite generation by @tsalo in https://github.com/PennLINC/xcp_d/pull/607

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.2.0...0.2.1

- Python
Published by tsalo over 3 years ago

xcp_d - 0.2.0

This is a big release. There are a lot of backwards-incompatible changes, as well as a number of bug-fixes and enhancements.

There is a full list of the changes made between 0.1.3 and 0.2.0 below. However, here are some highlights:

We have renamed and reorganized a number of the outputs created by xcp_d to better follow BIDS convention. There is a lot in xcp_d that falls outside the current BIDS specification, so we took inspiration from a number of BIDS Extension Proposals (BEPs) that folks have written over the years.
There is a new --warp-surfaces-native2std flag, which produces a number of subject-specific surfaces in fsLR space. This was previously run by default in version 0.1.3. The workflow that this flag triggers is also much improved, thanks to @madisoth.
We have fixed a major bug, in which the parameter set users selected was ignored, and "36P" was used no matter what.
The HTML reports have been improved. The interactive segmentation image from the executive summary has been added to the main report, along with the BOLD-T1w coregistration figure. We have also added a new plot to show the impact of filtering motion parameters on censoring.

What's Changed

🛠 Breaking Changes

Ensure TSV files are tab-delimited by @tsalo in https://github.com/PennLINC/xcp_d/pull/541
Rename derivatives to be more BIDS-compliant by @tsalo in https://github.com/PennLINC/xcp_d/pull/553
Replace --func-only with --warp-surfaces-native2std by @tsalo in https://github.com/PennLINC/xcp_d/pull/562
Add headers to motion.tsv and outliers.tsv files by @tsalo in https://github.com/PennLINC/xcp_d/pull/587 ### 🎉 Exciting New Features
Create dataset description file by @tsalo in https://github.com/PennLINC/xcp_d/pull/561
Distinguish preprocessed dataset formats by @tsalo in https://github.com/PennLINC/xcp_d/pull/567
Output temporal mask by @tsalo in https://github.com/PennLINC/xcp_d/pull/586
Add censoring plot to summary reports by @tsalo in https://github.com/PennLINC/xcp_d/pull/579
Add existing SVG figures and brainplot HTML figure to HTML report by @tsalo in https://github.com/PennLINC/xcp_d/pull/590
Output all filtered motion parameters by @tsalo in https://github.com/PennLINC/xcp_d/pull/592
Deprecate --bandpass_filter in favor of --disable-bandpass-filter by @tsalo in https://github.com/PennLINC/xcp_d/pull/588 ### 👎 Deprecations
Deprecate nuissance-regressors in favor of nuisance-regressors by @tsalo in https://github.com/PennLINC/xcp_d/pull/513 ### 🐛 Bug Fixes
Fix fsLR32k reg and ApplyWarpfield issues by @madisoth in https://github.com/PennLINC/xcp_d/pull/442
Replace MIT license with BSD-3 by @tsalo in https://github.com/PennLINC/xcp_d/pull/457
Update utils.py to fix MNILin6 imports by @smeisler in https://github.com/PennLINC/xcp_d/pull/458
Potential fix for "no tasks found" problem by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/464
Fix "manadatory" typo in interfaces by @tsalo in https://github.com/PennLINC/xcp_d/pull/540
Change "hpc" in CLI to "hcp" by @tsalo in https://github.com/PennLINC/xcp_d/pull/560
Pin pybids to version 0.15.1 by @madisoth in https://github.com/PennLINC/xcp_d/pull/537
Fix resampling of fsnative structural surfaces to fsLR by @madisoth in https://github.com/PennLINC/xcp_d/pull/496
Fix documentation and validation of motion filtering parameters by @tsalo in https://github.com/PennLINC/xcp_d/pull/575
Show framewise displacement before filtering in QCPlot by @tsalo in https://github.com/PennLINC/xcp_d/pull/581
Fix concatenation code w.r.t. recent output changes by @tsalo in https://github.com/PennLINC/xcp_d/pull/593
Use user-requested parameters in regression by @tsalo in https://github.com/PennLINC/xcp_d/pull/596
Update loadaroma so the correct file is being read in by @kahinimehta in https://github.com/PennLINC/xcpd/pull/599 ### Other Changes
Rf/smoothing by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/415
Rf/misc. by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/421
Rf/fconts by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/424
[RF] Miscellaneous by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/439
[RF] Reho Computation by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/437
[DOC] Update docs by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/433
[RF] ALFF Computation by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/435
[RF] fixes by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/443
[RF] Executive summary by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/445
[RF] Compute qcplot.py by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/447
[RF] Make TR tests shorter by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/462
[DOC] Add badges to README by @tsalo in https://github.com/PennLINC/xcp_d/pull/466
[DOC] Add issue templates and route to NeuroStars by @tsalo in https://github.com/PennLINC/xcp_d/pull/465
[REF] Use nilearn for loading and masking nifti data by @tsalo in https://github.com/PennLINC/xcp_d/pull/459
[TST] Add linting GH workflow by @tsalo in https://github.com/PennLINC/xcp_d/pull/467
[DOC] Address formatting issues in documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/469
[REF] Replace all relative imports with absolute ones by @tsalo in https://github.com/PennLINC/xcp_d/pull/472
[FIX] Address failing RTD build by @tsalo in https://github.com/PennLINC/xcp_d/pull/477
[REF] Use f-strings consistently throughout codebase by @tsalo in https://github.com/PennLINC/xcp_d/pull/473
[DOC] Use welcome bot to comment on new contributors' PRs by @tsalo in https://github.com/PennLINC/xcp_d/pull/475
[RF] Linting by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/479
[DOC] Add or format docstrings throughout package by @tsalo in https://github.com/PennLINC/xcp_d/pull/474
[REF] Lint interfaces by @tsalo in https://github.com/PennLINC/xcp_d/pull/480
[REF] Lint workflows by @tsalo in https://github.com/PennLINC/xcp_d/pull/481
[REF] Lint utils by @tsalo in https://github.com/PennLINC/xcp_d/pull/485
[REF] Rename functions to snakecase by @tsalo in https://github.com/PennLINC/xcpd/pull/487
[REF] Rename classes to CamelCase by @tsalo in https://github.com/PennLINC/xcp_d/pull/486
[RF] Get rid of unused variables by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/493
[DOC] Add docstrings to CLI module by @tsalo in https://github.com/PennLINC/xcp_d/pull/490
[REF] Address remaining linter warnings by @tsalo in https://github.com/PennLINC/xcp_d/pull/494
[REF] Move functions and classes into appropriate modules by @tsalo in https://github.com/PennLINC/xcp_d/pull/489
[DOC] Add API to documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/498
[DOC] Clean up workflow docstrings by @tsalo in https://github.com/PennLINC/xcp_d/pull/503
[REF] Remove duplicate functions by @tsalo in https://github.com/PennLINC/xcp_d/pull/502
[REF] Empty init.py files by @tsalo in https://github.com/PennLINC/xcp_d/pull/499
[REF] Centralize DerivativesDataSink definition by @tsalo in https://github.com/PennLINC/xcp_d/pull/510
[MAINT] Add CITATION.cff file by @tsalo in https://github.com/PennLINC/xcp_d/pull/482
[TST] Store CircleCI artifacts by @tsalo in https://github.com/PennLINC/xcp_d/pull/521
[REF] Start replacing common parameters with filldoc by @tsalo in https://github.com/PennLINC/xcpd/pull/509
[REF] Remove the notebooks module by @tsalo in https://github.com/PennLINC/xcp_d/pull/531
[DOC] Add TemplateFlow citation to boilerplate by @tsalo in https://github.com/PennLINC/xcp_d/pull/520
[DOC] Use sphinxcontrib-bibtex to embed BibTeX references in documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/516
[TST] Make local tests stricter by @tsalo in https://github.com/PennLINC/xcp_d/pull/545
[TST] Check for existence of outputs in tests by @tsalo in https://github.com/PennLINC/xcp_d/pull/542
[REF] Remove FSL from dependencies by @tsalo in https://github.com/PennLINC/xcp_d/pull/528
[TST] Restructure local patch handling in testing setup by @tsalo in https://github.com/PennLINC/xcp_d/pull/550
[REF] Simplify BOLD/CIFTI post-processing workflow call by @tsalo in https://github.com/PennLINC/xcp_d/pull/534
[REF] Remove unused initpostprocesswf by @tsalo in https://github.com/PennLINC/xcpd/pull/535
[REF] Use MapNodes to simplify functional connectivity workflows by @tsalo in https://github.com/PennLINC/xcp_d/pull/546
Add release notes template by @tsalo in https://github.com/PennLINC/xcp_d/pull/552
Add warning to documentation about M1 chip by @tsalo in https://github.com/PennLINC/xcp_d/pull/572
Improve confound plot readability and fix moving registration plot by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/530
Fix the local pytest script and documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/564
[TEST] Add tests for outstanding modules by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/529
[FIX] Fcon workflow tests are incompatible with changes from main by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/584

New Contributors

@tsalo made their first contribution in https://github.com/PennLINC/xcp_d/pull/457

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.1.3...0.2.0

- Python
Published by tsalo over 3 years ago

xcp_d - v0.1.3

What's Changed

Add analysis-level option
Quick fix for bugs in bold and cifti workflow

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.1.2...0.1.3

- Python
Published by kahinimehta over 3 years ago

xcp_d - v0.1.2

What's Changed

Fix malloc failure by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/395
[RF] Filtering by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/390
Rf/rename by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/398
Rf/rename by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/400
Rf/rename by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/401
[RF] Smoothing by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/404

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.1.1...0.1.2

- Python
Published by kahinimehta over 3 years ago

xcp_d - v0.1.1

What's Changed

Replace NiPype's filemanip.py by @madisoth in https://github.com/PennLINC/xcp_d/pull/383
[RF] Fix typos by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/386
ENH: Update filemanip.py "specialextensions" with the rest of the CIFTI-2 multi-part extensions by @madisoth in https://github.com/PennLINC/xcpd/pull/388
[RF] Interpolation by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/387
FIX: reho / writegii by @madisoth in https://github.com/PennLINC/xcpd/pull/385

Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.1.0...0.1.1

- Python
Published by kahinimehta over 3 years ago

xcp_d - 0.1.0

Additional features for surface processing and expanded CI testing

- Python
Published by mattcieslak over 3 years ago

xcp_d - 0.0.9

Now supports Schaefer 100,200,300,400,500,600,700,800,900,1000
CompCor fix, where previously we were not including cosine
Removed Temporal CompCor; no one should use this anyways
Added aromagsr and compcorgsr, which include global signal regression
Huge update of the documentation
This is the handoff update from @a3sha2 to @mb3152

- Python
Published by mb3152 about 4 years ago

xcp_d - 0.0.8

afni-reho-despike correction

What's Changed

Hcpdcan by @a3sha2 in https://github.com/PennLINC/xcp_abcd/pull/211
Hcpdcan by @a3sha2 in https://github.com/PennLINC/xcp_abcd/pull/212

Full Changelog: https://github.com/PennLINC/xcp_abcd/compare/0.0.7...0.0.8

- Python
Published by a3sha2 over 4 years ago

xcp_d - nthread/mem_gb in nipype pluggin

What's Changed

Hcpdcan by @a3sha2 in https://github.com/PennLINC/xcp_abcd/pull/181
Hcpdcan by @a3sha2 in https://github.com/PennLINC/xcp_abcd/pull/182
Hcpdcan by @a3sha2 in https://github.com/PennLINC/xcp_abcd/pull/183
thread/meggb included in plugin settings by @a3sha2 in https://github.com/PennLINC/xcpabcd/pull/184
nthread/ompthread by @a3sha2 in https://github.com/PennLINC/xcp_abcd/pull/185
remove labelled by @a3sha2 in https://github.com/PennLINC/xcp_abcd/pull/186
increased bold memgb size by @a3sha2 in https://github.com/PennLINC/xcp_abcd/pull/187
Hcpdcan by @a3sha2 in https://github.com/PennLINC/xcp_abcd/pull/194

Full Changelog: https://github.com/PennLINC/xcp_abcd/compare/0.0.6...0.0.7

- Python
Published by a3sha2 over 4 years ago

xcp_d - hcp/dcan

anatomical update executive summary dcan ingression

- Python
Published by a3sha2 over 4 years ago

xcp_d - nibabiestest

NIBABIES TEST - [x] MNI152NLin6Asym template for nibabies #156 - [x] update executive summary and report #69 #115 #157 #151 - [x] anatomical workflow added including freesurfer/freesurfer* - [x] outputs for cifti and nifti

- Python
Published by a3sha2 over 4 years ago

xcp_d - final release for hcp

- Python
Published by a3sha2 over 4 years ago

xcp_d - hcp

- Python
Published by a3sha2 over 4 years ago

xcp_d - second release

- Python
Published by a3sha2 over 4 years ago

xcp_d - initial release

- Python
Published by a3sha2 almost 5 years ago

Recent Releases of xcp_d

xcp_d - 0.11.1

What's Changed

🐛 Bug Fixes

xcp_d - 0.11.0

What's Changed

🛠 Breaking Changes

xcp_d - 0.11.0rc1

What's Changed

🛠 Breaking Changes

xcp_d - 0.10.7

What's Changed

🎉 Exciting New Features

xcp_d - 0.10.6

What's Changed

🎉 Exciting New Features

New Contributors

xcp_d - 0.10.5

What's Changed

🎉 Exciting New Features

xcp_d - 0.10.4

What's Changed

🐛 Bug Fixes

xcp_d - 0.10.3

What's Changed

🐛 Bug Fixes

xcp_d - 0.10.2

What's Changed

🐛 Bug Fixes

Other Changes

xcp_d - 0.10.1

What's Changed

🐛 Bug Fixes

xcp_d - 0.10.0

What's Changed

🛠 Breaking Changes

xcp_d - 0.10.0rc3

What's Changed

🐛 Bug Fixes

xcp_d - 0.10.0rc2

What's Changed

🛠 Breaking Changes

xcp_d - 0.10.0rc1

What's Changed

🛠 Breaking Changes

xcp_d - 0.9.1

What's Changed

Other Changes

xcp_d - 0.9.0

What's Changed

🛠 Breaking Changes

🎉 Exciting New Features

🐛 Bug Fixes

xcp_d - 0.8.3

What's Changed

🐛 Bug Fixes

xcp_d - 0.8.2

What's Changed

🎉 Exciting New Features

xcp_d - 0.8.1

What's Changed

🐛 Bug Fixes

xcp_d - 0.8.0

What's Changed

🛠 Breaking Changes

🎉 Exciting New Features

🐛 Bug Fixes

Other Changes

xcp_d - 0.7.5

What's Changed

🐛 Bug Fixes

xcp_d - 0.7.4

What's Changed

🎉 Exciting New Features

🐛 Bug Fixes

Other Changes

xcp_d - 0.7.3

What's Changed

🐛 Bug Fixes

xcp_d - 0.7.2