What's Changed

• FIX: Pin latest NiReports release (24.0.2) addressing fMRIPlot issues by @oesteban (#1342)
• FIX: Edge artifacts in first and last slices due to interpolation by @oesteban (#1338)
• FIX: Normalize bids-filters' modality keys to be lowercase by @oesteban (#1332)
• ENH: Add license NOTICE to start banner by @oesteban (#1343)
• ENH: Enable writing crashfiles in compressed-pickle format by @oesteban (#1339)
• ENH: Use orjson to serialize JSON, addressing Numpy serialization issues by @oesteban (#1337)
• ENH: Handle WebAPI timeouts more gently by @oesteban (#1336)

Full Changelog: 24.0.1...24.0.2

Release Notes

A patch release with a large number of bugfixes (mostly focusing on memory issues), maintenance activities, and the crawling of metadata before Nipype kicks in as a major optimization.

What's Changed

• FIX: Multiecho fMRI crashing with 'unhashable type' errors by @oesteban in #1295
• FIX: Set n_procs instead of num_threads on node apply_hmc by @oesteban in #1309
• FIX: Address memory issues by limiting BigPlot's parallelization. by @oesteban in #1320
• FIX: Address memory issues in DWI pipeline by @oesteban in #1323
• FIX: Limit IQMs' node number of processes and therefore, memory by @oesteban in #1325
• FIX: Resolve numeric overflow in drift estimation node by @oesteban in #1324
• FIX: Revise bugfix #1324 by @oesteban in #1327
• FIX: Remove unreachable code within DWI pipeline by @oesteban in #1328
• ENH: Allow moving the cache folder with an environment variable by @oesteban in #1285
• ENH: Flatten multi-echo lists in circumstances that they fail by @oesteban in #1286
• ENH: Added type hints to config module by @zvi-quantivly in #1288
• ENH: Add test for the CLI parser by @jhlegarreta in #1293
• ENH: Add CLI entry point test by @jhlegarreta in #1294
• ENH: Add development dockerfile for testing local changes to repo. by @rwblair in #1299
• ENH: Crawl dataset's metadata only once and before Nipype's workflow by @oesteban in #1317
• ENH(dMRI): Deal gracefully with small CC masks by @oesteban in #1311
• ENH: Leverage new spun-off apply interface by @oesteban in #1313
• MAINT: Removed personal infromation from maintainers and updated in contributors by @zvi-quantivly in #1289
• MAINT: Add JHLegarreta to contributors list by @jhlegarreta in #1301
• MAINT: Flexibilize pandas pinned version by @oesteban in #1310
• MAINT: Remove Pandas's FutureWarning by @oesteban in #1326
• DOC: Add description of summary_fg to the documentation by @celprov in #1306
• STY: Apply ruff/flake8-implicit-str-concat rule ISC001 by @DimitriPapadopoulos in #1296
• STY: Format Jupyter notebooks by @oesteban in #1321

New Contributors

• @jhlegarreta made their first contribution in #1293

Full Changelog: 24.0.0...24.0.1

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
• FIX: Revise config save/load and update inputs after dropping by @oesteban in #1245
• ENH: Expose a command-line option for minimum DWI volumes by @oesteban in #1249
• FIX: Skip short BOLD runs that break outlier detection by @effigies in #1120
• MAINT: Prevent pandas-originating deprecation warning by @oesteban in #1251
• ENH: Improve logging of runtime by @oesteban in #1253
• ENH: Improve documentation and logging of SynthStrip's model by @oesteban in #1254
• MAINT: Clean up more FutureWarning issued by pandas by @oesteban in #1257
• ENH: Mechanism to protect config's fields and write out config by @oesteban in #1258
• FIX: Make sure new logs and config file output are compatible with parallel processes by @oesteban in #1259
• FIX: Select filters if modalities are selected by @oesteban in #1261
• FIX: Address issues that had broken the group reports by @oesteban in #1262
• FIX: Enable group reports for DWI by @oesteban in #1266
• Removed pre-commit from development dependencies by @zvi-quantivly in #1269
• FIX: Finalized naming and connection of DWI IQMs by @oesteban in #1272
• MAINT: Added ruff to development dependencies by @zvi-quantivly in #1271
• FIX: Calculation of trivial shells by @oesteban in #1276
• STY: Applied ruff formatting by @zvi-quantivly in #1273
• ENH: Annotate nodes with n_procs to allow safe parallelization by @oesteban in #1277
• FIX: Remove DataLad as a node by @oesteban in #1278
• STY: Reformat with ruff by @oesteban in #1279
• Fail for non-formatted code by @zvi-quantivly in #1274
• REL: 24.0.0rc8 by @oesteban in #1280
• FIX: Bug in toml loader crashing with mixed arrays in config by @oesteban in #1281

New Contributors

• @araikes made their first contribution in #1211
• @zvi-quantivly made their first contribution in #1269

Full Changelog: 23.1.1...24.0.0

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
• FIX: Revise config save/load and update inputs after dropping by @oesteban in #1245
• ENH: Expose a command-line option for minimum DWI volumes by @oesteban in #1249
• FIX: Skip short BOLD runs that break outlier detection by @effigies in #1120
• MAINT: Prevent pandas-originating deprecation warning by @oesteban in #1251
• ENH: Improve logging of runtime by @oesteban in #1253
• ENH: Improve documentation and logging of SynthStrip's model by @oesteban in #1254
• MAINT: Clean up more FutureWarning issued by pandas by @oesteban in #1257
• ENH: Mechanism to protect config's fields and write out config by @oesteban in #1258
• FIX: Make sure new logs and config file output are compatible with parallel processes by @oesteban in #1259
• FIX: Select filters if modalities are selected by @oesteban in #1261
• FIX: Address issues that had broken the group reports by @oesteban in #1262
• FIX: Enable group reports for DWI by @oesteban in #1266
• Removed pre-commit from development dependencies by @zvi-quantivly in #1269
• FIX: Finalized naming and connection of DWI IQMs by @oesteban in #1272
• MAINT: Added ruff to development dependencies by @zvi-quantivly in #1271
• FIX: Calculation of trivial shells by @oesteban in #1276
• STY: Applied ruff formatting by @zvi-quantivly in #1273
• ENH: Annotate nodes with n_procs to allow safe parallelization by @oesteban in #1277
• FIX: Remove DataLad as a node by @oesteban in #1278
• STY: Reformat with ruff by @oesteban in #1279
• Fail for non-formatted code by @zvi-quantivly in #1274

New Contributors

• @araikes made their first contribution in #1211
• @zvi-quantivly made their first contribution in #1269

Full Changelog: 23.1.1...24.0.0rc8

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
• FIX: Revise config save/load and update inputs after dropping by @oesteban in #1245
• ENH: Expose a command-line option for minimum DWI volumes by @oesteban in #1249
• FIX: Skip short BOLD runs that break outlier detection by @effigies in #1120
• MAINT: Prevent pandas-originating deprecation warning by @oesteban in #1251
• ENH: Improve logging of runtime by @oesteban in #1253
• ENH: Improve documentation and logging of SynthStrip's model by @oesteban in #1254
• MAINT: Clean up more FutureWarning issued by pandas by @oesteban in #1257
• ENH: Mechanism to protect config's fields and write out config by @oesteban in #1258
• FIX: Make sure new logs and config file output are compatible with parallel processes by @oesteban in #1259
• FIX: Select filters if modalities are selected by @oesteban in #1261
• FIX: Address issues that had broken the group reports by @oesteban in #1262
• FIX: Enable group reports for DWI by @oesteban in #1266
• Removed pre-commit from development dependencies by @zvi-quantivly in #1269
• FIX: Finalized naming and connection of DWI IQMs by @oesteban in #1272

New Contributors

• @araikes made their first contribution in #1211
• @zvi-quantivly made their first contribution in #1269

Full Changelog: 23.1.1...24.0.0rc7

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
• FIX: Revise config save/load and update inputs after dropping by @oesteban in #1245
• ENH: Expose a command-line option for minimum DWI volumes by @oesteban in #1249
• FIX: Skip short BOLD runs that break outlier detection by @effigies in #1120
• MAINT: Prevent pandas-originating deprecation warning by @oesteban in #1251
• ENH: Improve logging of runtime by @oesteban in #1253
• ENH: Improve documentation and logging of SynthStrip's model by @oesteban in #1254
• MAINT: Clean up more FutureWarning issued by pandas by @oesteban in #1257
• ENH: Mechanism to protect config's fields and write out config by @oesteban in #1258
• FIX: Make sure new logs and config file output are compatible with parallel processes by @oesteban in #1259

New Contributors

• @araikes made their first contribution in #1211

Full Changelog: 23.1.1...24.0.0rc6

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
• FIX: Revise config save/load and update inputs after dropping by @oesteban in #1245
• ENH: Expose a command-line option for minimum DWI volumes by @oesteban in #1249
• FIX: Skip short BOLD runs that break outlier detection by @effigies in #1120
• MAINT: Prevent pandas-originating deprecation warning by @oesteban in #1251
• ENH: Improve logging of runtime by @oesteban in #1253
• ENH: Improve documentation and logging of SynthStrip's model by @oesteban in #1254
• MAINT: Clean up more FutureWarning issued by pandas by @oesteban in #1257
• ENH: Mechanism to protect config's fields and write out config by @oesteban in #1258

New Contributors

• @araikes made their first contribution in #1211

Full Changelog: 23.1.1...24.0.0rc5

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
• FIX: Revise config save/load and update inputs after dropping by @oesteban in #1245
• ENH: Expose a command-line option for minimum DWI volumes by @oesteban in #1249
• FIX: Skip short BOLD runs that break outlier detection by @effigies in #1120

New Contributors

• @araikes made their first contribution in #1211

Full Changelog: 23.1.1...24.0.0rc4

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...24.0.0rc3

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