24.0.0rc2

What's Changed

• FIX: Typo in sorted(..., reverse=True) call by @araikes in #1211
• MAINT: Update contributor affiliation in CONTRIBUTORS.md by @oesteban in #1214
• CI: flake8 → ruff check by @DimitriPapadopoulos in #1212
• DOC: Add changelog to documentation by @oesteban in #1217
• ENH: Revise summary stats extraction and include controlled roundings by @oesteban in #1219
• ENH: Adds diffusion-related IQMs. by @arokem in #1131
• ENH: Add computation of spiking voxels mask and percent IQMs by @oesteban in #1224
• ENH: Add FA-based IQMs (nans percentage and degenerate percentage) by @oesteban in #1225
• ENH: Add new IQM for DWI -- NDC by @oesteban in #1226
• ENH: Use MAD for robust estimation of sigma in the CC mask by @oesteban in #1228
• ENH: Integrate PIESNO noise mask and sigma estimation by @oesteban in #1227
• ENH: Noise floor estimated with PCA (dwidenoise) as an IQM by @oesteban in #1229
• ENH: Move from DTI to DKI with multishell data by @oesteban in #1230
• ENH: Add b-vector angular deviations as IQMs by @oesteban in #1233
• FIX: Duplicate node in anatomical workflow by @oesteban in #1234
• ENH: Improve error handling and logging by @oesteban in #1238
• FIX: Avert costly BIDSLayout.__repr__ calls when saving config by @oesteban in #1239
• FIX: Exclude DWI runs with insufficient orientations or missing bvals by @oesteban in #1240
• FIX: Handle NUMEXPR_MAX_THREADS like OMP_NUM_THREADS by @oesteban in #1241
• FIX: Drift should not be estimated when less than three low-b volumes present by @oesteban in #1242
• FIX: Sloppy merge by @oesteban in #1243

New Contributors

• @araikes made their first contribution in #1211

Full Changelog: 23.1.1...24.0.0rc2

24.0.0rc1

What's Changed

• FIX: Typo in sorted(..., reverse=True) call by @araikes in #1211
• MAINT: Update contributor affiliation in CONTRIBUTORS.md by @oesteban in #1214
• CI: flake8 → ruff check by @DimitriPapadopoulos in #1212
• DOC: Add changelog to documentation by @oesteban in #1217
• ENH: Revise summary stats extraction and include controlled roundings by @oesteban in #1219
• ENH: Adds diffusion-related IQMs. by @arokem in #1131
• ENH: Add computation of spiking voxels mask and percent IQMs by @oesteban in #1224
• ENH: Add FA-based IQMs (nans percentage and degenerate percentage) by @oesteban in #1225
• ENH: Add new IQM for DWI -- NDC by @oesteban in #1226
• ENH: Use MAD for robust estimation of sigma in the CC mask by @oesteban in #1228
• ENH: Integrate PIESNO noise mask and sigma estimation by @oesteban in #1227
• ENH: Noise floor estimated with PCA (dwidenoise) as an IQM by @oesteban in #1229
• ENH: Move from DTI to DKI with multishell data by @oesteban in #1230
• ENH: Add b-vector angular deviations as IQMs by @oesteban in #1233
• FIX: Duplicate node in anatomical workflow by @oesteban in #1234

New Contributors

• @araikes made their first contribution in #1211

Full Changelog: 23.1.1...24.0.0rc1

23.1.1

Release Notes

A long-overdue hotfix release addressing many bugs generated during the development of the new dMRI workflows and some relating to improvements in handling multi-echo fMRI.
The release also includes one year of maintenance actions and a general code cleanup with Ruff.

What's Changed

• FIX: Missing connection to head-motion estimation node in DWI workflow by @oesteban in #1207
• FIX: Revise porting to Loader by @oesteban in #1201
• FIX: Revise the last two sloppy merges by @oesteban in #1200
• FIX: Move from pkg_resources to niworkflows.data.Loader by @oesteban in #1199
• FIX: DIPY not listed as a dependency by @oesteban in #1197
• FIX: Include dwidenoise within Docker image by @oesteban in #1196
• FIX: Copy name attribute of dataset_description.json from input dataset by @celprov in #1187
• FIX: Remove FD as an iterfield in MapNode causing crash with ME-BOLD by @celprov in #1179
• FIX: Incorrect plugin metadata passed to Report Assembler by @oesteban in #1188
• FIX: Temporary fix of the missing "dwi" key by @celprov in #1174
• FIX: Rearrange multi-echo report by @celprov in #1164
• FIX: Typo in inputnode field in dMRI masking workflow by @celprov in #1165
• FIX: Bug in group level workflow by @celprov in #1148
• FIX: Bugs in DWI workflow by @celprov in #1147
• FIX: Use simpler DWI reference workflow by @yibeichan in #1145
• FIX: Drop deprecated Networkx's API by @celprov in #1137
• FIX: Replace np.float by np.float64 by @celprov in #1140
• ENH: Improved logging and optimize early checkpoint on subjects by @oesteban in #1198
• ENH: Store confound timeseries data by @psadil in #1166
• ENH: Large overhaul of the functional workflow w/focus on ME-EPI by @oesteban in #1155
• ENH: Implement BIDS filters file and drop legacy BIDS querying by @oesteban in #1154
• ENH: Swap background and zoomed-in visualizations in anatomical reports by @oesteban in #1151
• MAINT: Test on Python 3.12 by @DimitriPapadopoulos in #1156
• MAINT: Disable flaky T1w test on CircleCI by @oesteban in #1202
• MAINT: Overhaul of the Dockerfile by @oesteban in #1195
• MAINT: Revise package's extra dependencies by @oesteban in #1194
• MAINT: Clean up some setuptools_scm remnants by @oesteban in #1193
• MAINT: Load FMRISummary from NiReports rather than NiWorkflows by @celprov in #1167
• MAINT: Update to latest migas' API by @mgxd in #1160
• MAINT: Update bold to large resource class in config.yml by @oesteban in #1158
• MAINT: Refresh cached intermediate results by @oesteban in #1143
• MAINT: Simplify GitHub actions checks and update action versions by @effigies in #1141
• MAINT: Python 3.11 is supported by @DimitriPapadopoulos in #1123
• MAINT: Apply suggestions from pyupgrade by @DimitriPapadopoulos in #1124
• DOC: Update Sphinx pinned version to 5 by @oesteban in #1192
• DOC: http:// → https:// by @DimitriPapadopoulos in #1126
• DOC: Add info on the FreeSurfer requirement for bare install to address #1034 by @neurorepro in #1130
• STY: Add Ruff config and fix all warnings and errors by @oesteban in #1203
• STY: Remove extraneous parentheses by @DimitriPapadopoulos in #1186
• STY: Apply a few refurb suggestions by @DimitriPapadopoulos in #1162
• STY: Fix typo found by codespell by @DimitriPapadopoulos in #1161

New Contributors

• @neurorepro made their first contribution in #1130
• @DimitriPapadopoulos made their first contribution in #1126
• @yibeichan made their first contribution in #1145

Full Changelog: 23.1.0...23.1.1

23.1.0

What's Changed

• MAINT: Update deprecated nibabel.spatialimage.get_data() calls by @oesteban in #1096
• ENH: Propagate logging level to subprocesses by @ZviBaratz in #1030
• ENH: Refactor reports system to use NiReports and the general VRS by @oesteban in #1085
• MAINT: Move codespell configuration to pyproject.toml by @oesteban in #1097
• ENH: Improving the resource monitor -- infer PID from process name by @esavary in #1049
• FIX: Separate report bootstrap files (anat vs. func) by @oesteban in #1098
• FIX: Test broken by #1098 by @oesteban in #1100
• ENH: Move templates' probsegs into individual at normalization by @oesteban in #1103
• FIX: Inform SynthStrip about the desired intraop threads by @oesteban in #1101
• ENH: Drop utilization of "head" mask from template by @oesteban in #1104
• ENH: Drop FSL BET to estimate the "outskin" (head) mask by @oesteban in #1105
• FIX: Refine the head mask after removal of FSL BET by @oesteban in #1107
• ENH: Drop FSL MELODIC (without alternative) by @oesteban in #1106
• FIX: Remove unused dipy import in the functional interfaces by @oesteban in #1109
• ENH: Replace FSL FAST with ANTs Atropos for brain tissue segmentation by @oesteban in #1099
• ENH: Culminate dropping FSL as a dependency by @oesteban in #1108
• FIX: BIDS database directory handling by @oesteban in #1110
• FIX: PlotMosaic expects lists, not tuples by @eilidhmacnicol in #1111
• FIX: Add protection for NaNs and INFs when calculating QI2 by @oesteban in #1112
• ENH: MRIQC for DWI by @oesteban in #1113
• ENH: Add a basic DTI fitting into the diffusion workflow by @oesteban in #1115
• ENH: More compact shell-wise summary statistic maps (avg/std) by @oesteban in #1116
• ENH: Incorporate new NiReports' DWI heatmaps by @oesteban in #1119

Full Changelog: 23.0.1...23.1.0

23.1.0rc0

What's Changed

• MAINT: Update deprecated nibabel.spatialimage.get_data() calls by @oesteban in #1096
• Propagate logging level to subprocesses by @ZviBaratz in #1030
• ENH: Refactor reports system to use NiReports and the general VRS by @oesteban in #1085

Full Changelog: 23.0.1...23.1.0rc0

23.0.1

What's Changed

• FIX: Input data has incompatible dimensionality (plotting ICA) by @oesteban in #1082
• ENH: Optimize metadata gathering reusing BIDSLayout db by @oesteban in #1084
• DOC : update anatomical example report in documentation by @celprov in #1088
• MAINT: Drop old mriqc_plot script by @oesteban in #1091
• FIX: Underspecified regex sets BIDSLayout to ignore data with sesions by @oesteban in #1094

Full Changelog: 23.0.0...23.0.1

23.0.0

What's Changed

• DOC: Fixes a couple of broken links to RTD nipype docs. by @arokem in #1040
• DOC : complete the documentation of summary_stats() by @celprov in #1044
• DOC : update documentation with the new carpetplot by @celprov in #1045
• MAINT: Rotate CircleCI secrets and setup up org-level context by @oesteban in #1046
• ENH: Add migas telemetry by @mgxd in #1036
• FIX: Resource monitor would not ever start tracking by @oesteban in #1051
• Codespell: config, action, and typos fixed by @yarikoptic in #1057
• MAINT: Update CircleCI executor and use built-in docker-compose by @oesteban in #1061
• MAINT: Add McKenzie to the maintainers table by @oesteban in #1059
• Add myself to CONTRIBUTORS by @yarikoptic in #1060
• FIX: Update T1w metrics by @oesteban in #1063
• FIX: Preempt PyBIDS to spend time indexing non-BIDS folders by @oesteban in #1050
• MAINT: Fix minor aspects of WebAPI deployment on CircleCI by @oesteban in #1064
• MAINT: Update niworkflows pin to support newer ANTs releases by @esavary in #1047
• MAINT: add @esavary as a contributor by @oesteban in #1066
• FIX: Move telemetry atexit into entrypoint func by @mgxd in #1067
• MAINT: Pin PyBIDS 0.15.6 (culminating #1050) by @oesteban in #1069
• MAINT: Migrate to hatchling by @oesteban in #1070
• MAINT: Conclude porting of reportlets into NiReports by @oesteban in #1068
• ENH: Add DataLad getter to inputs of functional workflows by @oesteban in #1071
• FIX: Uniformize building workflow message (anat vs. func) by @oesteban in #1072
• MAINT: Move Zvi to maintainers list by @oesteban in #1074
• MAINT: Add Ariel to contributors and PIs by @oesteban in #1073
• MAINT: Add Patrick Sadil to contributors by @oesteban in #1075
• MAINT: Move Eilidh from contributors to maintainers by @oesteban in #1076
• FIX: Address non-empty take from empty axes (anatomical IQMs) by @oesteban in #1077
• MAINT: Pacify codespell by @oesteban in #1080
• MAINT: Update NiReports calls to upcoming interfaces API by @oesteban in #1078
• FIX: orientation of visualisations when species == "rat" by @eilidhmacnicol in #1027

New Contributors

• @arokem made their first contribution in #1040
• @yarikoptic made their first contribution in #1057
• @esavary made their first contribution in #1047

Full Changelog: 22.0.6...23.0.0

23.0.0rc1

What's Changed

• ENH: Add DataLad getter to inputs of functional workflows by @oesteban in #1071
• FIX: Uniformize building workflow message (anat vs. func) by @oesteban in #1072

Full Changelog: 23.0.0rc0...23.0.0rc1

23.0.0rc0

What's Changed

• DOC: Fixes a couple of broken links to RTD nipype docs. by @arokem in #1040
• DOC : complete the documentation of summary_stats() by @celprov in #1044
• DOC : update documentation with the new carpetplot by @celprov in #1045
• MAINT: Rotate CircleCI secrets and setup up org-level context by @oesteban in #1046
• ENH: Add migas telemetry by @mgxd in #1036
• FIX: Resource monitor would not ever start tracking by @oesteban in #1051
• Codespell: config, action, and typos fixed by @yarikoptic in #1057
• MAINT: Update CircleCI executor and use built-in docker-compose by @oesteban in #1061
• MAINT: Add McKenzie to the maintainers table by @oesteban in #1059
• Add myself to CONTRIBUTORS by @yarikoptic in #1060
• FIX: Update T1w metrics by @oesteban in #1063
• FIX: Preempt PyBIDS to spend time indexing non-BIDS folders by @oesteban in #1050
• MAINT: Fix minor aspects of WebAPI deployment on CircleCI by @oesteban in #1064
• MAINT: Update niworkflows pin to support newer ANTs releases by @esavary in #1047
• MAINT: add @esavary as a contributor by @oesteban in #1066
• FIX: Move telemetry atexit into entrypoint func by @mgxd in #1067
• MAINT: Pin PyBIDS 0.15.6 (culminating #1050) by @oesteban in #1069
• MAINT: Migrate to hatchling by @oesteban in #1070
• MAINT: Conclude porting of reportlets into NiReports by @oesteban in #1068

New Contributors

• @arokem made their first contribution in #1040
• @yarikoptic made their first contribution in #1057
• @esavary made their first contribution in #1047

Full Changelog: 22.0.6...23.0.0rc0

22.0.6

What's Changed

• FIX: Better fix to the multi-argument --participant-label issue by @oesteban in #1026

Full Changelog: 22.0.5...22.0.6