Whatβs Newο
0.7.2ο
This is a patch release fixing small bugs in 0.7.1.
π Exciting New Featuresο
Make
GeneratedBy
in preprocessing derivativesβdataset_description.json
optional by @tsalo in https://github.com/PennLINC/xcp_d/pull/1151
π Bug Fixesο
Fix exit code bug in
cli.run.main()
by @tsalo in https://github.com/PennLINC/xcp_d/pull/1152
Other Changesο
Replace pkgrf with load_data by @tsalo in https://github.com/PennLINC/xcp_d/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/0.7.1β¦0.7.2
0.7.1ο
This release prepares for the XCP-D manuscript.
π Breaking Changesο
Change default
--min-time
from 100 to 240 by @tsalo in https://github.com/PennLINC/xcp_d/pull/1115
π Exciting New Featuresο
Add
--bids-database-dir
parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/1116Ignore subcortical figures and plot FOV center of reference brains in executive summary by @tsalo in https://github.com/PennLINC/xcp_d/pull/1145
π Bug Fixesο
Modify metadata and boilerplate to reflect updated motion filter parameters by @tsalo in https://github.com/PennLINC/xcp_d/pull/1114
Add βsubjectβ 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/1122Pin 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 Changesο
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/0.7.0β¦0.7.1
0.7.0ο
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.
π Breaking Changesο
[DCAN] Remove
--dcan-qc
parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/1096Bring outputs up to date with BEPs 11, 12, 17, and 38 by @tsalo in https://github.com/PennLINC/xcp_d/pull/1065
Stop appending βxcp_dβ to output directory by @tsalo in https://github.com/PennLINC/xcp_d/pull/1061
π Exciting New Featuresο
Create reformatted BrainSwipes figures for HBCD QC by @tsalo in https://github.com/PennLINC/xcp_d/pull/1091
Other Changesο
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/0.6.4β¦0.7.0
0.6.4ο
π Exciting New Featuresο
Replace
bids:xcp_d:
BIDS URI withbids::
by @tsalo in https://github.com/PennLINC/xcp_d/pull/1088
π Deprecationsο
[DCAN] Enable DCAN QC by default by @tsalo in https://github.com/PennLINC/xcp_d/pull/1086
π Bug Fixesο
Raise error if atlas affines donβt 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/1092Adopt Lindquist-compliant denoising method by @tsalo in https://github.com/PennLINC/xcp_d/pull/1087
Other Changesο
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/0.6.3β¦0.6.4
0.6.3ο
π Exciting New Featuresο
Make βDatasetTypeβ key recommended, not required by @tsalo in https://github.com/PennLINC/xcp_d/pull/1068
π Bug Fixesο
Do not warn if
fd-thresh
andmin-time
are both set to 0 by @tsalo in https://github.com/PennLINC/xcp_d/pull/1071Use
copy_atlas
to write out atlas tsv and json files by @tsalo in https://github.com/PennLINC/xcp_d/pull/1073Raise error if FS_LICENSE environment variable is not an existing file by @tsalo in https://github.com/PennLINC/xcp_d/pull/1072
Generate T2w executive summary plots when T1w is also available by @tsalo in https://github.com/PennLINC/xcp_d/pull/1078
Other Changesο
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/0.6.2β¦0.6.3
0.6.2ο
π Bug Fixesο
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 collect_run_data 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 Changesο
Make description of
smoothing
parameter clearer when set to0
by @psychelzh in https://github.com/PennLINC/xcp_d/pull/1056
Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.6.1β¦0.6.2
0.6.1ο
π Breaking Changesο
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
π Exciting New Featuresο
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
π Bug Fixesο
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/1037Fix 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 Changesο
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 Contributorsο
@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/0.6.0β¦0.6.1
0.6.0ο
π Breaking Changesο
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/966Replace AtlasPack 0.0.5 atlases with AtlasPack 0.1.0 atlases by @tsalo in https://github.com/PennLINC/xcp_d/pull/991
π Exciting New Featuresο
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
π Bug Fixesο
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
Donβt 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
Donβt 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 Changesο
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
Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.5.0β¦0.6.0
0.5.1ο
The 0.5.1 fixes some bugs for the XCP-D manuscript.
π Breaking Changesο
Update the QC metrics by @tsalo in https://github.com/PennLINC/xcp_d/pull/958
π Exciting New Featuresο
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
π Bug Fixesο
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
Donβt interpolate volumes at beginning/end of run by @tsalo in https://github.com/PennLINC/xcp_d/pull/950
Other Changesο
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/0.5.0β¦0.5.1
0.5.0ο
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).
π Breaking Changesο
Add CIFTI subcortical atlas to XCP-D by @tsalo in https://github.com/PennLINC/xcp_d/pull/864
Change βciftiSubcorticalβ atlas name to βHCPβ by @tsalo in https://github.com/PennLINC/xcp_d/pull/932
π Exciting New Featuresο
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 βnoneβ 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/885Allow white matter surface suffix to be either β_smoothwmβ or β_whiteβ 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/930Generate executive summary figures without
--dcan-qc
by @tsalo in https://github.com/PennLINC/xcp_d/pull/936
π Bug Fixesο
Standardize executive summary carpet if params is βnoneβ 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 Changesο
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 xcp_d.utils.utils module by @tsalo in https://github.com/PennLINC/xcp_d/pull/910
Add tests for xcp_d.utils.execsummary module by @tsalo in https://github.com/PennLINC/xcp_d/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/04.0β¦0.5.0
0.4.0ο
π Breaking Changesο
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/753Change QC filenames and fix
xcp_d-combineqc
command-line interface by @tsalo in https://github.com/PennLINC/xcp_d/pull/762Retain 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/770Zero 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/836Remove deprecated
--dummytime
parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/837Change 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
π Exciting New Featuresο
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/782Improve 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
π Bug Fixesο
Replace missing verticesβ 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/766Check for existence of dataset_description.json in fmri_dir 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 load_confounds aCompCor bug by @tsalo in https://github.com/PennLINC/xcp_d/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 Changesο
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/761Add 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 prepare_confounds and denoise_bold 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/0.3.2β¦04.0
0.3.2ο
This release adopts a workbench show-scene-based brainsprite for the executive summary. It also removes the brainsprite figure from the nipreps report.
π Exciting New Featuresο
Adopt executive summaryβs brainsprite using jinja templates by @tsalo in https://github.com/PennLINC/xcp_d/pull/702
Other Changesο
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/0.3.1β¦0.3.2
0.3.1ο
π Breaking Changesο
Remove
--nuissance-regressors
and--bandpass_filter
by @tsalo in https://github.com/PennLINC/xcp_d/pull/658
π Exciting New Featuresο
Add
--dummy-scans
parameter and deprecate--dummytime
by @tsalo in https://github.com/PennLINC/xcp_d/pull/616Add
--bids-filter-file
parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/686Enable 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
π Bug Fixesο
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 load_aroma by @tsalo in https://github.com/PennLINC/xcp_d/pull/670
Use input_type to determine order of preferred spaces by @tsalo in https://github.com/PennLINC/xcp_d/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/695Downcast >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 Changesο
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 donβt 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/0.3.0β¦0.3.1
0.3.0ο
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.
π Breaking Changesο
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/650Support custom confounds with headers by @tsalo in https://github.com/PennLINC/xcp_d/pull/642
π Exciting New Featuresο
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
π Bug Fixesο
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 Changesο
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/0.2.0β¦0.3.0
0.2.2ο
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.
π Exciting New Featuresο
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
π Bug Fixesο
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 Changesο
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/0.2.1β¦0.2.2
0.2.1ο
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.
π Breaking Changesο
Output ReHo as a CIFTI by @tsalo in https://github.com/PennLINC/xcp_d/pull/601
π Exciting New Featuresο
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
π Bug Fixesο
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 Changesο
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/0.2.0β¦0.2.1
0.2.0ο
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 inxcp_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 β36Pβ 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.
π Breaking Changesο
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/562Add headers to motion.tsv and outliers.tsv files by @tsalo in https://github.com/PennLINC/xcp_d/pull/587
π Exciting New Featuresο
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
π Deprecationsο
Deprecate nuissance-regressors in favor of nuisance-regressors by @tsalo in https://github.com/PennLINC/xcp_d/pull/513
π Bug Fixesο
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 βno tasks foundβ problem by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/464
Fix βmanadatoryβ typo in interfaces by @tsalo in https://github.com/PennLINC/xcp_d/pull/540
Change βhpcβ in CLI to βhcpβ 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 load_aroma so the correct file is being read in by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/599
Other Changesο
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 contributorsβ 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 snake_case by @tsalo in https://github.com/PennLINC/xcp_d/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 fill_doc by @tsalo in https://github.com/PennLINC/xcp_d/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 init_post_process_wf by @tsalo in https://github.com/PennLINC/xcp_d/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 Contributorsο
@tsalo made their first contribution in https://github.com/PennLINC/xcp_d/pull/457
Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.1.3β¦0.2.0
0.1.3ο
Add analysis-level option
Quick fix for bugs in bold and cifti workflow
Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.1.2β¦0.1.3
0.1.2ο
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/0.1.1β¦0.1.2
0.1.1ο
Replace NiPypeβs 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 βspecial_extensionsβ with the rest of the CIFTI-2 multi-part extensions by @madisoth in https://github.com/PennLINC/xcp_d/pull/388
[RF] Interpolation by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/387
FIX: reho / write_gii by @madisoth in https://github.com/PennLINC/xcp_d/pull/385
Full Changelog: https://github.com/PennLINC/xcp_d/compare/0.1.0β¦0.1.1
0.1.0ο
Additional features for surface processing and expanded CI testing
0.0.9ο
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 aroma_gsr and compcor_gsr, which include global signal regression
Huge update of the documentation
This is the handoff update from @a3sha2 to @mb3152
0.0.8ο
afni-reho-despike correction
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/0.0.7β¦0.0.8
0.0.7ο
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/meg_gb included in plugin settings by @a3sha2 in https://github.com/PennLINC/xcp_abcd/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/0.0.6β¦0.0.7
0.0.6ο
anatomical update executive summary dcan ingression
0.0.5ο
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
0.0.4ο
final release for hcp
0.0.3ο
hcp Update cifti.py
0.0.2ο
Merge pull request #113 from PennLINC/template
Template
0.0.1ο
Merge pull request #64 from PennLINC/test_xcp
add version automatically