What's Changed

FIX: Optimize interface to minimize memory fingerprint by @oesteban in https://github.com/nipreps/mriqc/pull/1351
FIX: Passing bytes into str.join() by @oesteban in https://github.com/nipreps/mriqc/pull/1356
ENH: Reorganize documentation and redirect to nipreps docs by @oesteban in https://github.com/nipreps/mriqc/pull/1367
doc: Fix missing code block start by @effigies in https://github.com/nipreps/mriqc/pull/1368
Provide a range of years ending with current for the copyright statement by @yarikoptic in https://github.com/nipreps/mriqc/pull/1359
ENH: Remove redundant DIPY function by @jhlegarreta in https://github.com/nipreps/mriqc/pull/1369
BUG: Fix elapsed runtime format by @jhlegarreta in https://github.com/nipreps/mriqc/pull/1366
FIX: Containers report wrong version by @oesteban in https://github.com/nipreps/mriqc/pull/1357
Add a HPC troubleshooting section to the documentation by @vferat in https://github.com/nipreps/mriqc/pull/1349
FIX: Decode bytes to produce a string by @oesteban in https://github.com/nipreps/mriqc/pull/1371
FIX: Containers report wrong version (revision) by @oesteban in https://github.com/nipreps/mriqc/pull/1372

New Contributors

@vferat made their first contribution in https://github.com/nipreps/mriqc/pull/1349

Full Changelog: https://github.com/nipreps/mriqc/compare/24.0.2...25.0.0rc0

- Python
Published by oesteban about 1 year ago

What's Changed

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

Full Changelog: https://github.com/nipreps/mriqc/compare/24.0.1...24.0.2

- Python
Published by oesteban over 1 year ago

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

New Contributors

@jhlegarreta made their first contribution in https://github.com/nipreps/mriqc/pull/1293

Full Changelog: https://github.com/nipreps/mriqc/compare/24.0.0...24.0.1

- Python
Published by oesteban over 1 year ago

What's Changed

FIX: Typo in sorted(..., reverse=True) call by @araikes in https://github.com/nipreps/mriqc/pull/1211
MAINT: Update contributor affiliation in CONTRIBUTORS.md by @oesteban in https://github.com/nipreps/mriqc/pull/1214
CI: flake8 → ruff check by @DimitriPapadopoulos in https://github.com/nipreps/mriqc/pull/1212
DOC: Add changelog to documentation by @oesteban in https://github.com/nipreps/mriqc/pull/1217
ENH: Revise summary stats extraction and include controlled roundings by @oesteban in https://github.com/nipreps/mriqc/pull/1219
ENH: Adds diffusion-related IQMs. by @arokem in https://github.com/nipreps/mriqc/pull/1131
ENH: Add computation of spiking voxels mask and percent IQMs by @oesteban in https://github.com/nipreps/mriqc/pull/1224
ENH: Add FA-based IQMs (nans percentage and degenerate percentage) by @oesteban in https://github.com/nipreps/mriqc/pull/1225
ENH: Add new IQM for DWI -- NDC by @oesteban in https://github.com/nipreps/mriqc/pull/1226
ENH: Use MAD for robust estimation of sigma in the CC mask by @oesteban in https://github.com/nipreps/mriqc/pull/1228
ENH: Integrate PIESNO noise mask and sigma estimation by @oesteban in https://github.com/nipreps/mriqc/pull/1227
ENH: Noise floor estimated with PCA (dwidenoise) as an IQM by @oesteban in https://github.com/nipreps/mriqc/pull/1229
ENH: Move from DTI to DKI with multishell data by @oesteban in https://github.com/nipreps/mriqc/pull/1230
ENH: Add b-vector angular deviations as IQMs by @oesteban in https://github.com/nipreps/mriqc/pull/1233
FIX: Duplicate node in anatomical workflow by @oesteban in https://github.com/nipreps/mriqc/pull/1234
ENH: Improve error handling and logging by @oesteban in https://github.com/nipreps/mriqc/pull/1238
FIX: Avert costly BIDSLayout.__repr__ calls when saving config by @oesteban in https://github.com/nipreps/mriqc/pull/1239
FIX: Exclude DWI runs with insufficient orientations or missing bvals by @oesteban in https://github.com/nipreps/mriqc/pull/1240
FIX: Handle NUMEXPR_MAX_THREADS like OMP_NUM_THREADS by @oesteban in https://github.com/nipreps/mriqc/pull/1241
FIX: Drift should not be estimated when less than three low-b volumes present by @oesteban in https://github.com/nipreps/mriqc/pull/1242
FIX: Sloppy merge by @oesteban in https://github.com/nipreps/mriqc/pull/1243
FIX: Revise config save/load and update inputs after dropping by @oesteban in https://github.com/nipreps/mriqc/pull/1245
ENH: Expose a command-line option for minimum DWI volumes by @oesteban in https://github.com/nipreps/mriqc/pull/1249
FIX: Skip short BOLD runs that break outlier detection by @effigies in https://github.com/nipreps/mriqc/pull/1120
MAINT: Prevent pandas-originating deprecation warning by @oesteban in https://github.com/nipreps/mriqc/pull/1251
ENH: Improve logging of runtime by @oesteban in https://github.com/nipreps/mriqc/pull/1253
ENH: Improve documentation and logging of SynthStrip's model by @oesteban in https://github.com/nipreps/mriqc/pull/1254
MAINT: Clean up more FutureWarning issued by pandas by @oesteban in https://github.com/nipreps/mriqc/pull/1257
ENH: Mechanism to protect config's fields and write out config by @oesteban in https://github.com/nipreps/mriqc/pull/1258
FIX: Make sure new logs and config file output are compatible with parallel processes by @oesteban in https://github.com/nipreps/mriqc/pull/1259
FIX: Select filters if modalities are selected by @oesteban in https://github.com/nipreps/mriqc/pull/1261
FIX: Address issues that had broken the group reports by @oesteban in https://github.com/nipreps/mriqc/pull/1262
FIX: Enable group reports for DWI by @oesteban in https://github.com/nipreps/mriqc/pull/1266
Removed pre-commit from development dependencies by @zvi-quantivly in https://github.com/nipreps/mriqc/pull/1269
FIX: Finalized naming and connection of DWI IQMs by @oesteban in https://github.com/nipreps/mriqc/pull/1272
MAINT: Added ruff to development dependencies by @zvi-quantivly in https://github.com/nipreps/mriqc/pull/1271
FIX: Calculation of trivial shells by @oesteban in https://github.com/nipreps/mriqc/pull/1276
STY: Applied ruff formatting by @zvi-quantivly in https://github.com/nipreps/mriqc/pull/1273
ENH: Annotate nodes with n_procs to allow safe parallelization by @oesteban in https://github.com/nipreps/mriqc/pull/1277
FIX: Remove DataLad as a node by @oesteban in https://github.com/nipreps/mriqc/pull/1278
STY: Reformat with ruff by @oesteban in https://github.com/nipreps/mriqc/pull/1279
Fail for non-formatted code by @zvi-quantivly in https://github.com/nipreps/mriqc/pull/1274
REL: 24.0.0rc8 by @oesteban in https://github.com/nipreps/mriqc/pull/1280
FIX: Bug in toml loader crashing with mixed arrays in config by @oesteban in https://github.com/nipreps/mriqc/pull/1281

New Contributors

@araikes made their first contribution in https://github.com/nipreps/mriqc/pull/1211
@zvi-quantivly made their first contribution in https://github.com/nipreps/mriqc/pull/1269

Full Changelog: https://github.com/nipreps/mriqc/compare/23.1.1...24.0.0

- Python
Published by oesteban almost 2 years ago

What's Changed

FIX: Typo in sorted(..., reverse=True) call by @araikes in https://github.com/nipreps/mriqc/pull/1211
MAINT: Update contributor affiliation in CONTRIBUTORS.md by @oesteban in https://github.com/nipreps/mriqc/pull/1214
CI: flake8 → ruff check by @DimitriPapadopoulos in https://github.com/nipreps/mriqc/pull/1212
DOC: Add changelog to documentation by @oesteban in https://github.com/nipreps/mriqc/pull/1217
ENH: Revise summary stats extraction and include controlled roundings by @oesteban in https://github.com/nipreps/mriqc/pull/1219
ENH: Adds diffusion-related IQMs. by @arokem in https://github.com/nipreps/mriqc/pull/1131
ENH: Add computation of spiking voxels mask and percent IQMs by @oesteban in https://github.com/nipreps/mriqc/pull/1224
ENH: Add FA-based IQMs (nans percentage and degenerate percentage) by @oesteban in https://github.com/nipreps/mriqc/pull/1225
ENH: Add new IQM for DWI -- NDC by @oesteban in https://github.com/nipreps/mriqc/pull/1226
ENH: Use MAD for robust estimation of sigma in the CC mask by @oesteban in https://github.com/nipreps/mriqc/pull/1228
ENH: Integrate PIESNO noise mask and sigma estimation by @oesteban in https://github.com/nipreps/mriqc/pull/1227
ENH: Noise floor estimated with PCA (dwidenoise) as an IQM by @oesteban in https://github.com/nipreps/mriqc/pull/1229
ENH: Move from DTI to DKI with multishell data by @oesteban in https://github.com/nipreps/mriqc/pull/1230
ENH: Add b-vector angular deviations as IQMs by @oesteban in https://github.com/nipreps/mriqc/pull/1233
FIX: Duplicate node in anatomical workflow by @oesteban in https://github.com/nipreps/mriqc/pull/1234
ENH: Improve error handling and logging by @oesteban in https://github.com/nipreps/mriqc/pull/1238
FIX: Avert costly BIDSLayout.__repr__ calls when saving config by @oesteban in https://github.com/nipreps/mriqc/pull/1239
FIX: Exclude DWI runs with insufficient orientations or missing bvals by @oesteban in https://github.com/nipreps/mriqc/pull/1240
FIX: Handle NUMEXPR_MAX_THREADS like OMP_NUM_THREADS by @oesteban in https://github.com/nipreps/mriqc/pull/1241
FIX: Drift should not be estimated when less than three low-b volumes present by @oesteban in https://github.com/nipreps/mriqc/pull/1242
FIX: Sloppy merge by @oesteban in https://github.com/nipreps/mriqc/pull/1243
FIX: Revise config save/load and update inputs after dropping by @oesteban in https://github.com/nipreps/mriqc/pull/1245
ENH: Expose a command-line option for minimum DWI volumes by @oesteban in https://github.com/nipreps/mriqc/pull/1249
FIX: Skip short BOLD runs that break outlier detection by @effigies in https://github.com/nipreps/mriqc/pull/1120
MAINT: Prevent pandas-originating deprecation warning by @oesteban in https://github.com/nipreps/mriqc/pull/1251
ENH: Improve logging of runtime by @oesteban in https://github.com/nipreps/mriqc/pull/1253
ENH: Improve documentation and logging of SynthStrip's model by @oesteban in https://github.com/nipreps/mriqc/pull/1254
MAINT: Clean up more FutureWarning issued by pandas by @oesteban in https://github.com/nipreps/mriqc/pull/1257
ENH: Mechanism to protect config's fields and write out config by @oesteban in https://github.com/nipreps/mriqc/pull/1258
FIX: Make sure new logs and config file output are compatible with parallel processes by @oesteban in https://github.com/nipreps/mriqc/pull/1259
FIX: Select filters if modalities are selected by @oesteban in https://github.com/nipreps/mriqc/pull/1261
FIX: Address issues that had broken the group reports by @oesteban in https://github.com/nipreps/mriqc/pull/1262
FIX: Enable group reports for DWI by @oesteban in https://github.com/nipreps/mriqc/pull/1266
Removed pre-commit from development dependencies by @zvi-quantivly in https://github.com/nipreps/mriqc/pull/1269
FIX: Finalized naming and connection of DWI IQMs by @oesteban in https://github.com/nipreps/mriqc/pull/1272
MAINT: Added ruff to development dependencies by @zvi-quantivly in https://github.com/nipreps/mriqc/pull/1271
FIX: Calculation of trivial shells by @oesteban in https://github.com/nipreps/mriqc/pull/1276
STY: Applied ruff formatting by @zvi-quantivly in https://github.com/nipreps/mriqc/pull/1273
ENH: Annotate nodes with n_procs to allow safe parallelization by @oesteban in https://github.com/nipreps/mriqc/pull/1277
FIX: Remove DataLad as a node by @oesteban in https://github.com/nipreps/mriqc/pull/1278
STY: Reformat with ruff by @oesteban in https://github.com/nipreps/mriqc/pull/1279
Fail for non-formatted code by @zvi-quantivly in https://github.com/nipreps/mriqc/pull/1274

New Contributors

@araikes made their first contribution in https://github.com/nipreps/mriqc/pull/1211
@zvi-quantivly made their first contribution in https://github.com/nipreps/mriqc/pull/1269

Full Changelog: https://github.com/nipreps/mriqc/compare/23.1.1...24.0.0rc8

- Python
Published by oesteban almost 2 years ago

What's Changed

FIX: Typo in sorted(..., reverse=True) call by @araikes in https://github.com/nipreps/mriqc/pull/1211
MAINT: Update contributor affiliation in CONTRIBUTORS.md by @oesteban in https://github.com/nipreps/mriqc/pull/1214
CI: flake8 → ruff check by @DimitriPapadopoulos in https://github.com/nipreps/mriqc/pull/1212
DOC: Add changelog to documentation by @oesteban in https://github.com/nipreps/mriqc/pull/1217
ENH: Revise summary stats extraction and include controlled roundings by @oesteban in https://github.com/nipreps/mriqc/pull/1219
ENH: Adds diffusion-related IQMs. by @arokem in https://github.com/nipreps/mriqc/pull/1131
ENH: Add computation of spiking voxels mask and percent IQMs by @oesteban in https://github.com/nipreps/mriqc/pull/1224
ENH: Add FA-based IQMs (nans percentage and degenerate percentage) by @oesteban in https://github.com/nipreps/mriqc/pull/1225
ENH: Add new IQM for DWI -- NDC by @oesteban in https://github.com/nipreps/mriqc/pull/1226
ENH: Use MAD for robust estimation of sigma in the CC mask by @oesteban in https://github.com/nipreps/mriqc/pull/1228
ENH: Integrate PIESNO noise mask and sigma estimation by @oesteban in https://github.com/nipreps/mriqc/pull/1227
ENH: Noise floor estimated with PCA (dwidenoise) as an IQM by @oesteban in https://github.com/nipreps/mriqc/pull/1229
ENH: Move from DTI to DKI with multishell data by @oesteban in https://github.com/nipreps/mriqc/pull/1230
ENH: Add b-vector angular deviations as IQMs by @oesteban in https://github.com/nipreps/mriqc/pull/1233
FIX: Duplicate node in anatomical workflow by @oesteban in https://github.com/nipreps/mriqc/pull/1234
ENH: Improve error handling and logging by @oesteban in https://github.com/nipreps/mriqc/pull/1238
FIX: Avert costly BIDSLayout.__repr__ calls when saving config by @oesteban in https://github.com/nipreps/mriqc/pull/1239
FIX: Exclude DWI runs with insufficient orientations or missing bvals by @oesteban in https://github.com/nipreps/mriqc/pull/1240
FIX: Handle NUMEXPR_MAX_THREADS like OMP_NUM_THREADS by @oesteban in https://github.com/nipreps/mriqc/pull/1241
FIX: Drift should not be estimated when less than three low-b volumes present by @oesteban in https://github.com/nipreps/mriqc/pull/1242
FIX: Sloppy merge by @oesteban in https://github.com/nipreps/mriqc/pull/1243
FIX: Revise config save/load and update inputs after dropping by @oesteban in https://github.com/nipreps/mriqc/pull/1245
ENH: Expose a command-line option for minimum DWI volumes by @oesteban in https://github.com/nipreps/mriqc/pull/1249
FIX: Skip short BOLD runs that break outlier detection by @effigies in https://github.com/nipreps/mriqc/pull/1120
MAINT: Prevent pandas-originating deprecation warning by @oesteban in https://github.com/nipreps/mriqc/pull/1251
ENH: Improve logging of runtime by @oesteban in https://github.com/nipreps/mriqc/pull/1253
ENH: Improve documentation and logging of SynthStrip's model by @oesteban in https://github.com/nipreps/mriqc/pull/1254
MAINT: Clean up more FutureWarning issued by pandas by @oesteban in https://github.com/nipreps/mriqc/pull/1257
ENH: Mechanism to protect config's fields and write out config by @oesteban in https://github.com/nipreps/mriqc/pull/1258
FIX: Make sure new logs and config file output are compatible with parallel processes by @oesteban in https://github.com/nipreps/mriqc/pull/1259
FIX: Select filters if modalities are selected by @oesteban in https://github.com/nipreps/mriqc/pull/1261
FIX: Address issues that had broken the group reports by @oesteban in https://github.com/nipreps/mriqc/pull/1262
FIX: Enable group reports for DWI by @oesteban in https://github.com/nipreps/mriqc/pull/1266
Removed pre-commit from development dependencies by @zvi-quantivly in https://github.com/nipreps/mriqc/pull/1269
FIX: Finalized naming and connection of DWI IQMs by @oesteban in https://github.com/nipreps/mriqc/pull/1272

New Contributors

@araikes made their first contribution in https://github.com/nipreps/mriqc/pull/1211
@zvi-quantivly made their first contribution in https://github.com/nipreps/mriqc/pull/1269

Full Changelog: https://github.com/nipreps/mriqc/compare/23.1.1...24.0.0rc7

- Python
Published by oesteban almost 2 years ago

What's Changed

FIX: Typo in sorted(..., reverse=True) call by @araikes in https://github.com/nipreps/mriqc/pull/1211
MAINT: Update contributor affiliation in CONTRIBUTORS.md by @oesteban in https://github.com/nipreps/mriqc/pull/1214
CI: flake8 → ruff check by @DimitriPapadopoulos in https://github.com/nipreps/mriqc/pull/1212
DOC: Add changelog to documentation by @oesteban in https://github.com/nipreps/mriqc/pull/1217
ENH: Revise summary stats extraction and include controlled roundings by @oesteban in https://github.com/nipreps/mriqc/pull/1219
ENH: Adds diffusion-related IQMs. by @arokem in https://github.com/nipreps/mriqc/pull/1131
ENH: Add computation of spiking voxels mask and percent IQMs by @oesteban in https://github.com/nipreps/mriqc/pull/1224
ENH: Add FA-based IQMs (nans percentage and degenerate percentage) by @oesteban in https://github.com/nipreps/mriqc/pull/1225
ENH: Add new IQM for DWI -- NDC by @oesteban in https://github.com/nipreps/mriqc/pull/1226
ENH: Use MAD for robust estimation of sigma in the CC mask by @oesteban in https://github.com/nipreps/mriqc/pull/1228
ENH: Integrate PIESNO noise mask and sigma estimation by @oesteban in https://github.com/nipreps/mriqc/pull/1227
ENH: Noise floor estimated with PCA (dwidenoise) as an IQM by @oesteban in https://github.com/nipreps/mriqc/pull/1229
ENH: Move from DTI to DKI with multishell data by @oesteban in https://github.com/nipreps/mriqc/pull/1230
ENH: Add b-vector angular deviations as IQMs by @oesteban in https://github.com/nipreps/mriqc/pull/1233
FIX: Duplicate node in anatomical workflow by @oesteban in https://github.com/nipreps/mriqc/pull/1234
ENH: Improve error handling and logging by @oesteban in https://github.com/nipreps/mriqc/pull/1238
FIX: Avert costly BIDSLayout.__repr__ calls when saving config by @oesteban in https://github.com/nipreps/mriqc/pull/1239
FIX: Exclude DWI runs with insufficient orientations or missing bvals by @oesteban in https://github.com/nipreps/mriqc/pull/1240
FIX: Handle NUMEXPR_MAX_THREADS like OMP_NUM_THREADS by @oesteban in https://github.com/nipreps/mriqc/pull/1241
FIX: Drift should not be estimated when less than three low-b volumes present by @oesteban in https://github.com/nipreps/mriqc/pull/1242
FIX: Sloppy merge by @oesteban in https://github.com/nipreps/mriqc/pull/1243
FIX: Revise config save/load and update inputs after dropping by @oesteban in https://github.com/nipreps/mriqc/pull/1245
ENH: Expose a command-line option for minimum DWI volumes by @oesteban in https://github.com/nipreps/mriqc/pull/1249
FIX: Skip short BOLD runs that break outlier detection by @effigies in https://github.com/nipreps/mriqc/pull/1120
MAINT: Prevent pandas-originating deprecation warning by @oesteban in https://github.com/nipreps/mriqc/pull/1251
ENH: Improve logging of runtime by @oesteban in https://github.com/nipreps/mriqc/pull/1253
ENH: Improve documentation and logging of SynthStrip's model by @oesteban in https://github.com/nipreps/mriqc/pull/1254
MAINT: Clean up more FutureWarning issued by pandas by @oesteban in https://github.com/nipreps/mriqc/pull/1257
ENH: Mechanism to protect config's fields and write out config by @oesteban in https://github.com/nipreps/mriqc/pull/1258
FIX: Make sure new logs and config file output are compatible with parallel processes by @oesteban in https://github.com/nipreps/mriqc/pull/1259

New Contributors

@araikes made their first contribution in https://github.com/nipreps/mriqc/pull/1211

Full Changelog: https://github.com/nipreps/mriqc/compare/23.1.1...24.0.0rc6

- Python
Published by oesteban almost 2 years ago

What's Changed

FIX: Typo in sorted(..., reverse=True) call by @araikes in https://github.com/nipreps/mriqc/pull/1211
MAINT: Update contributor affiliation in CONTRIBUTORS.md by @oesteban in https://github.com/nipreps/mriqc/pull/1214
CI: flake8 → ruff check by @DimitriPapadopoulos in https://github.com/nipreps/mriqc/pull/1212
DOC: Add changelog to documentation by @oesteban in https://github.com/nipreps/mriqc/pull/1217
ENH: Revise summary stats extraction and include controlled roundings by @oesteban in https://github.com/nipreps/mriqc/pull/1219
ENH: Adds diffusion-related IQMs. by @arokem in https://github.com/nipreps/mriqc/pull/1131
ENH: Add computation of spiking voxels mask and percent IQMs by @oesteban in https://github.com/nipreps/mriqc/pull/1224
ENH: Add FA-based IQMs (nans percentage and degenerate percentage) by @oesteban in https://github.com/nipreps/mriqc/pull/1225
ENH: Add new IQM for DWI -- NDC by @oesteban in https://github.com/nipreps/mriqc/pull/1226
ENH: Use MAD for robust estimation of sigma in the CC mask by @oesteban in https://github.com/nipreps/mriqc/pull/1228
ENH: Integrate PIESNO noise mask and sigma estimation by @oesteban in https://github.com/nipreps/mriqc/pull/1227
ENH: Noise floor estimated with PCA (dwidenoise) as an IQM by @oesteban in https://github.com/nipreps/mriqc/pull/1229
ENH: Move from DTI to DKI with multishell data by @oesteban in https://github.com/nipreps/mriqc/pull/1230
ENH: Add b-vector angular deviations as IQMs by @oesteban in https://github.com/nipreps/mriqc/pull/1233
FIX: Duplicate node in anatomical workflow by @oesteban in https://github.com/nipreps/mriqc/pull/1234
ENH: Improve error handling and logging by @oesteban in https://github.com/nipreps/mriqc/pull/1238
FIX: Avert costly BIDSLayout.__repr__ calls when saving config by @oesteban in https://github.com/nipreps/mriqc/pull/1239
FIX: Exclude DWI runs with insufficient orientations or missing bvals by @oesteban in https://github.com/nipreps/mriqc/pull/1240
FIX: Handle NUMEXPR_MAX_THREADS like OMP_NUM_THREADS by @oesteban in https://github.com/nipreps/mriqc/pull/1241
FIX: Drift should not be estimated when less than three low-b volumes present by @oesteban in https://github.com/nipreps/mriqc/pull/1242
FIX: Sloppy merge by @oesteban in https://github.com/nipreps/mriqc/pull/1243
FIX: Revise config save/load and update inputs after dropping by @oesteban in https://github.com/nipreps/mriqc/pull/1245
ENH: Expose a command-line option for minimum DWI volumes by @oesteban in https://github.com/nipreps/mriqc/pull/1249
FIX: Skip short BOLD runs that break outlier detection by @effigies in https://github.com/nipreps/mriqc/pull/1120
MAINT: Prevent pandas-originating deprecation warning by @oesteban in https://github.com/nipreps/mriqc/pull/1251
ENH: Improve logging of runtime by @oesteban in https://github.com/nipreps/mriqc/pull/1253
ENH: Improve documentation and logging of SynthStrip's model by @oesteban in https://github.com/nipreps/mriqc/pull/1254
MAINT: Clean up more FutureWarning issued by pandas by @oesteban in https://github.com/nipreps/mriqc/pull/1257
ENH: Mechanism to protect config's fields and write out config by @oesteban in https://github.com/nipreps/mriqc/pull/1258

New Contributors

@araikes made their first contribution in https://github.com/nipreps/mriqc/pull/1211

Full Changelog: https://github.com/nipreps/mriqc/compare/23.1.1...24.0.0rc5

- Python
Published by oesteban almost 2 years ago

What's Changed

FIX: Typo in sorted(..., reverse=True) call by @araikes in https://github.com/nipreps/mriqc/pull/1211
MAINT: Update contributor affiliation in CONTRIBUTORS.md by @oesteban in https://github.com/nipreps/mriqc/pull/1214
CI: flake8 → ruff check by @DimitriPapadopoulos in https://github.com/nipreps/mriqc/pull/1212
DOC: Add changelog to documentation by @oesteban in https://github.com/nipreps/mriqc/pull/1217
ENH: Revise summary stats extraction and include controlled roundings by @oesteban in https://github.com/nipreps/mriqc/pull/1219
ENH: Adds diffusion-related IQMs. by @arokem in https://github.com/nipreps/mriqc/pull/1131
ENH: Add computation of spiking voxels mask and percent IQMs by @oesteban in https://github.com/nipreps/mriqc/pull/1224
ENH: Add FA-based IQMs (nans percentage and degenerate percentage) by @oesteban in https://github.com/nipreps/mriqc/pull/1225
ENH: Add new IQM for DWI -- NDC by @oesteban in https://github.com/nipreps/mriqc/pull/1226
ENH: Use MAD for robust estimation of sigma in the CC mask by @oesteban in https://github.com/nipreps/mriqc/pull/1228
ENH: Integrate PIESNO noise mask and sigma estimation by @oesteban in https://github.com/nipreps/mriqc/pull/1227
ENH: Noise floor estimated with PCA (dwidenoise) as an IQM by @oesteban in https://github.com/nipreps/mriqc/pull/1229
ENH: Move from DTI to DKI with multishell data by @oesteban in https://github.com/nipreps/mriqc/pull/1230
ENH: Add b-vector angular deviations as IQMs by @oesteban in https://github.com/nipreps/mriqc/pull/1233
FIX: Duplicate node in anatomical workflow by @oesteban in https://github.com/nipreps/mriqc/pull/1234
ENH: Improve error handling and logging by @oesteban in https://github.com/nipreps/mriqc/pull/1238
FIX: Avert costly BIDSLayout.__repr__ calls when saving config by @oesteban in https://github.com/nipreps/mriqc/pull/1239
FIX: Exclude DWI runs with insufficient orientations or missing bvals by @oesteban in https://github.com/nipreps/mriqc/pull/1240
FIX: Handle NUMEXPR_MAX_THREADS like OMP_NUM_THREADS by @oesteban in https://github.com/nipreps/mriqc/pull/1241
FIX: Drift should not be estimated when less than three low-b volumes present by @oesteban in https://github.com/nipreps/mriqc/pull/1242
FIX: Sloppy merge by @oesteban in https://github.com/nipreps/mriqc/pull/1243
FIX: Revise config save/load and update inputs after dropping by @oesteban in https://github.com/nipreps/mriqc/pull/1245
ENH: Expose a command-line option for minimum DWI volumes by @oesteban in https://github.com/nipreps/mriqc/pull/1249
FIX: Skip short BOLD runs that break outlier detection by @effigies in https://github.com/nipreps/mriqc/pull/1120

New Contributors

@araikes made their first contribution in https://github.com/nipreps/mriqc/pull/1211

Full Changelog: https://github.com/nipreps/mriqc/compare/23.1.1...24.0.0rc4

- Python
Published by oesteban almost 2 years ago

What's Changed

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

New Contributors

@araikes made their first contribution in https://github.com/nipreps/mriqc/pull/1211

Full Changelog: https://github.com/nipreps/mriqc/compare/23.1.1...24.0.0rc3

- Python
Published by oesteban almost 2 years ago

What's Changed

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

New Contributors

@araikes made their first contribution in https://github.com/nipreps/mriqc/pull/1211

Full Changelog: https://github.com/nipreps/mriqc/compare/23.1.1...24.0.0rc2

- Python
Published by oesteban almost 2 years ago

What's Changed

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

New Contributors

@araikes made their first contribution in https://github.com/nipreps/mriqc/pull/1211

Full Changelog: https://github.com/nipreps/mriqc/compare/23.1.1...24.0.0rc1

- Python
Published by oesteban almost 2 years ago

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

New Contributors

@neurorepro made their first contribution in https://github.com/nipreps/mriqc/pull/1130
@DimitriPapadopoulos made their first contribution in https://github.com/nipreps/mriqc/pull/1126
@yibeichan made their first contribution in https://github.com/nipreps/mriqc/pull/1145

Full Changelog: https://github.com/nipreps/mriqc/compare/23.1.0...23.1.1

- Python
Published by oesteban almost 2 years ago

mriqc - 23.1.0

What's Changed

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

Full Changelog: https://github.com/nipreps/mriqc/compare/23.0.1...23.1.0

- Python
Published by oesteban over 2 years ago

mriqc - 23.1.0rc0

What's Changed

MAINT: Update deprecated nibabel.spatialimage.get_data() calls by @oesteban in https://github.com/nipreps/mriqc/pull/1096
Propagate logging level to subprocesses by @ZviBaratz in https://github.com/nipreps/mriqc/pull/1030
ENH: Refactor reports system to use NiReports and the general VRS by @oesteban in https://github.com/nipreps/mriqc/pull/1085

Full Changelog: https://github.com/nipreps/mriqc/compare/23.0.1...23.1.0rc0

- Python
Published by oesteban almost 3 years ago

mriqc - 23.0.1

What's Changed

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

Full Changelog: https://github.com/nipreps/mriqc/compare/23.0.0...23.0.1

- Python
Published by oesteban almost 3 years ago

mriqc - 23.0.0

What's Changed

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

New Contributors

@arokem made their first contribution in https://github.com/nipreps/mriqc/pull/1040
@yarikoptic made their first contribution in https://github.com/nipreps/mriqc/pull/1057
@esavary made their first contribution in https://github.com/nipreps/mriqc/pull/1047

Full Changelog: https://github.com/nipreps/mriqc/compare/22.0.6...23.0.0

- Python
Published by oesteban almost 3 years ago

mriqc - 23.0.0rc1

What's Changed

ENH: Add DataLad getter to inputs of functional workflows by @oesteban in https://github.com/nipreps/mriqc/pull/1071
FIX: Uniformize building workflow message (anat vs. func) by @oesteban in https://github.com/nipreps/mriqc/pull/1072

Full Changelog: https://github.com/nipreps/mriqc/compare/23.0.0rc0...23.0.0rc1

- Python
Published by oesteban almost 3 years ago

mriqc - 23.0.0rc0

What's Changed

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

New Contributors

@arokem made their first contribution in https://github.com/nipreps/mriqc/pull/1040
@yarikoptic made their first contribution in https://github.com/nipreps/mriqc/pull/1057
@esavary made their first contribution in https://github.com/nipreps/mriqc/pull/1047

Full Changelog: https://github.com/nipreps/mriqc/compare/22.0.6...23.0.0rc0

- Python
Published by oesteban almost 3 years ago

mriqc - 22.0.6

What's Changed

FIX: Better fix to the multi-argument --participant-label issue by @oesteban in https://github.com/nipreps/mriqc/pull/1026

Full Changelog: https://github.com/nipreps/mriqc/compare/22.0.5...22.0.6

- Python
Published by oesteban over 3 years ago

mriqc - 22.0.5

What's Changed

FIX: Multiple valued --participant-label wrongly parsed by @oesteban in https://github.com/nipreps/mriqc/pull/1025

Full Changelog: https://github.com/nipreps/mriqc/compare/22.0.4...22.0.5

- Python
Published by oesteban over 3 years ago

mriqc - 22.0.4

What's Changed

ENH: Bump Docker base to latest release by @oesteban in https://github.com/nipreps/mriqc/pull/1022
FIX: Major improvements to new datalad-based interface & perform within containers by @oesteban in https://github.com/nipreps/mriqc/pull/1024

Full Changelog: https://github.com/nipreps/mriqc/compare/22.0.3...22.0.4

- Python
Published by oesteban over 3 years ago

mriqc - 22.0.3

What's Changed

MAINT: Fix failing tests as python setup.py is deprecated by @oesteban in https://github.com/nipreps/mriqc/pull/1013
MAINT: Update the T1w IQMs to the new reference after #997 by @oesteban in https://github.com/nipreps/mriqc/pull/1014
ENH: New version of the rating widget by @oesteban in https://github.com/nipreps/mriqc/pull/1012
MAINT: Several critical updates to CircleCI and Docker images by @oesteban in https://github.com/nipreps/mriqc/pull/1016
MAINT: Fix statsmodels dependency, it is not optional by @oesteban in https://github.com/nipreps/mriqc/pull/1017
DOC: Move readthedocs to use the config v2 file (YAML) by @oesteban in https://github.com/nipreps/mriqc/pull/1018
set rat-specific defaults for FD calculations by @eilidhmacnicol in https://github.com/nipreps/mriqc/pull/1005
ENH: Add a new DataladIdentityInterface by @oesteban in https://github.com/nipreps/mriqc/pull/1020
remove slice-timing correction by @psadil in https://github.com/nipreps/mriqc/pull/1019
FIX: SynthStrip preprocessing miscalculating new shape after reorientation by @oesteban in https://github.com/nipreps/mriqc/pull/1021

New Contributors

@psadil made their first contribution in https://github.com/nipreps/mriqc/pull/1019

Full Changelog: https://github.com/nipreps/mriqc/compare/22.0.1...22.0.3

- Python
Published by oesteban over 3 years ago

mriqc - 22.0.2

What's Changed

MAINT: Fix failing tests as python setup.py is deprecated by @oesteban in https://github.com/nipreps/mriqc/pull/1013
MAINT: Update the T1w IQMs to the new reference after #997 by @oesteban in https://github.com/nipreps/mriqc/pull/1014
ENH: New version of the rating widget by @oesteban in https://github.com/nipreps/mriqc/pull/1012
MAINT: Several critical updates to CircleCI and Docker images by @oesteban in https://github.com/nipreps/mriqc/pull/1016
MAINT: Fix statsmodels dependency, it is not optional by @oesteban in https://github.com/nipreps/mriqc/pull/1017
DOC: Move readthedocs to use the config v2 file (YAML) by @oesteban in https://github.com/nipreps/mriqc/pull/1018

Full Changelog: https://github.com/nipreps/mriqc/compare/22.0.1...22.0.2

- Python
Published by oesteban over 3 years ago

mriqc - 22.0.1

What's Changed

FIX: More lenient handling of skull-stripped datasets by @oesteban in https://github.com/nipreps/mriqc/pull/997

Full Changelog: https://github.com/nipreps/mriqc/compare/22.0.0...22.0.1

- Python
Published by oesteban almost 4 years ago

mriqc - 22.0.0

Release Notes

First official release after migrating the repository into the NiPreps' organization. A major new feature is the rodent pipeline by Eilidh MacNicol (@eilidhmacnicol). A second major feature is the adoption of the updated carpet plots for BOLD fMRI, contributed by Céline Provins (@celprov). Virtual memory allocation has been ten-fold cut down, and a complementary resource monitor instrumentation is now available with MRIQC. This release updates the Docker image with up-to-date dependencies, updates MRIQC's codebase to the latest NiTransforms and includes some minor bugfixes. The code, modules and data related to the MRIQC classifier have been extracted into an isolated package called MRIQC-learn. Finally, this release also contains a major code style overhaul by Zvi Baratz.

The contributor/author crediting system has been adapted to the current draft of the NiPreps Community Governance documents.

With thanks to @ZviBaratz, @nbeliy, @octomike, @benkay86, @verdurin, @leej3, @utooley, and @jAchtzehn for their contributions.

CHANGES

FIX: Inconsistent API in anatomical CNR computation (#995)
FIX: Check sanity of input data before extracting IQMs (#994)
FIX: Plot segmentations after dropping off-diagonal (#989)
FIX: Replace all deprecated nibabel.get_data() in anatomical module (#988)
FIX: Resource profiler was broken with config file (#981)
FIX: preserve WM segments in rodents (#979)
FIX: Pin jinja2 < 3.1 (#978)
FIX: Make toml config unique, works around #912 (#960)
FIX: Nipype multiproc plugin expects n_procs and not nprocs (#961)
FIX: Set TR when generating carpetplots (enables time for X axis) (#971)
FIX: template_resolution deprecation warning (#941)
FIX: Set entity datatype in BIDSLayout queries (#942)
FIX: T2w image of MNI template unavailable in Singularity (#940)
FIX: Release process -- Docker deployment not working + Python package lacks WebAPI token (#938)
FIX: Revise building documentation at RTD after migration (#935)
FIX: Final touch-ups in the maintenance of Docker image + CI (#928)
FIX: Update unit tests (#927)
FIX: Update dependencies and repair BOLD workflow accordingly (#926)
FIX: Update dependencies and repair T1w workflow accordingly (#925)
FIX: Set matplotlib on Agg output mode (#892)
ENH: Deprecate --start-idx / --stop-idx (#993)
ENH: Add SynthStrip base module (#987)
ENH: Improve building workflow message feedback (#990)
ENH: Add instrumentation to monitor resources (#984)
ENH: Standalone, lightweight version of MultiProc plugin (#985)
ENH: Revise plugin and workflow initialization (#983)
ENH: Base generalization of the pipeline for rodents (#969)
ENH: Update to new NiWorkflows' API, which adds the crown to the carpetplot (#968)
ENH: Optimize PyBIDS' layout initialization (#939)
ENH: Refactored long strings to a :mod:mriqc.messages module (#901)
ENH: Refactored :mod:mriqc.interfaces.common module (#901)
DOC: Improve documentation of --nprocs and --omp-nthreads (#986)
DOC: Add sbatch file example for SLURM execution (#963)
DOC: Various fixes to "Running mriqc" section (#897)
MAINT: Refactor Dockerfile using new miniconda image (#974)
MAINT: Outsource the classifier into nipreps/mriqc-learn (#973)
MAINT: Update CONTRIBUTORS.md (#953)
MAINT: Update contributer location (#952)
MAINT: Updates to CONTRIBUTORS.md file
MAINT: Revise Docker image settings & CircleCI (#937)
MAINT: Finalize transfer to nipreps organization (#936)
MAINT: Relicensing to Apache-2.0, for compliance with NiPreps and prior transfer to the org (#930)
MAINT: New Docker layer caching system of other NiPreps (#929)
MAINT: Code style overhaul (#901)
MAINT: Update Dockerfile and catch-up with fMRIPrep's (#924)
STY: Run black at the top of the repo (#932)

Full Changelog: https://github.com/nipreps/mriqc/compare/0.16.1...22.0.0

- Python
Published by oesteban almost 4 years ago

mriqc - 22.0.0rc1

What's Changed

DOC: Tiny "Running mriqc" docs fix by @ZviBaratz in https://github.com/nipreps/mriqc/pull/897
FIX: TCL and display error by @nbeliy in https://github.com/nipreps/mriqc/pull/892
MAINT: Miscellaneous updates by @ZviBaratz in https://github.com/nipreps/mriqc/pull/901
MAINT: Update Dockerfile and catch-up with fMRIPrep's by @oesteban in https://github.com/nipreps/mriqc/pull/924
FIX: Update dependencies and repair T1w workflow accordingly by @oesteban in https://github.com/nipreps/mriqc/pull/925
FIX: Update dependencies and repair BOLD workflow accordingly by @oesteban in https://github.com/nipreps/mriqc/pull/926
FIX: Update unit tests by @oesteban in https://github.com/nipreps/mriqc/pull/927
FIX: Final touch-ups in the maintenance of Docker image + CI by @oesteban in https://github.com/nipreps/mriqc/pull/928
MAINT: New Docker layer caching system of other NiPreps by @oesteban in https://github.com/nipreps/mriqc/pull/929
STY: Run black at the top of the repo by @oesteban in https://github.com/nipreps/mriqc/pull/932
MAINT: Relicensing to Apache-2.0, for compliance with NiPreps and prior transfer to the org by @oesteban in https://github.com/nipreps/mriqc/pull/930
FIX: Revise building documentation at RTD after migration by @oesteban in https://github.com/nipreps/mriqc/pull/935
MAINT: Finalize transfer to nipreps organization by @oesteban in https://github.com/nipreps/mriqc/pull/936
MAINT: Revise Docker image settings & CircleCI by @oesteban in https://github.com/nipreps/mriqc/pull/937
FIX: Release process -- Docker deployment not working + Python package lacks WebAPI token by @oesteban in https://github.com/nipreps/mriqc/pull/938
FIX: T2w image of MNI template unavailable in Singularity by @oesteban in https://github.com/nipreps/mriqc/pull/940
ENH: Optimize PyBIDS' layout initialization by @oesteban in https://github.com/nipreps/mriqc/pull/939
FIX: Set entity datatype in BIDSLayout queries by @oesteban in https://github.com/nipreps/mriqc/pull/942
FIX: template_resolution deprecation warning by @oesteban in https://github.com/nipreps/mriqc/pull/941
MAINT: Updating contributor info per request by @justbennet in https://github.com/nipreps/mriqc/pull/944
MAINT: Update affiliations by @Shotgunosine in https://github.com/nipreps/mriqc/pull/945
MAINT: Add @pvelasco's ORCID by @pvelasco in https://github.com/nipreps/mriqc/pull/946
MAINT: Remove @apiccirilli by @apiccirilli in https://github.com/nipreps/mriqc/pull/948
MAINT: Update CONTRIBUTORS.md by @ZviBaratz in https://github.com/nipreps/mriqc/pull/947
MAINT: Update contributer location by @jdkent in https://github.com/nipreps/mriqc/pull/952
MAINT: Update CONTRIBUTORS.md by @leej3 in https://github.com/nipreps/mriqc/pull/953
DOC: Add sbatch file example for SLURM execution by @celprov in https://github.com/nipreps/mriqc/pull/963
ENH: Update to new niworkflows' API, which adds the crown to the carpetplot by @celprov in https://github.com/nipreps/mriqc/pull/968
FIX: Set TR when generating carpetplots (enables time for X axis) by @oesteban in https://github.com/nipreps/mriqc/pull/971
FIX: Nipype multiproc plugin expects n_procs and not nprocs by @octomike in https://github.com/nipreps/mriqc/pull/961
MAINT: Outsource the classifier into nipreps/mriqc-learn by @oesteban in https://github.com/nipreps/mriqc/pull/973
FIX: Make toml config unique, works around #912 by @octomike in https://github.com/nipreps/mriqc/pull/960
MAINT: Refactor Dockerfile using new miniconda image by @oesteban in https://github.com/nipreps/mriqc/pull/974

New Contributors

@ZviBaratz made their first contribution in https://github.com/nipreps/mriqc/pull/897
@nbeliy made their first contribution in https://github.com/nipreps/mriqc/pull/892
@leej3 made their first contribution in https://github.com/nipreps/mriqc/pull/953
@celprov made their first contribution in https://github.com/nipreps/mriqc/pull/963

Full Changelog: https://github.com/nipreps/mriqc/compare/0.16.1...22.0.0rc1

- Python
Published by oesteban almost 4 years ago

mriqc - 21.0.0rc2

- Python
Published by oesteban over 4 years ago

mriqc - 21.0.0rc1

- Python
Published by oesteban over 4 years ago

mriqc - 21.0.0rc0

- Python
Published by oesteban over 4 years ago

mriqc - 0.16.1

Release Notes

Bug-fix release in 0.16.x series.

This PR improves BIDS Derivatives compliance, fixes an issue with reading datasets with subjects of the form sub-sXYZ, and improves compatibility with more recent matplotlib.

CHANGES

FIX: Participant labels starting with [sub] cannot be used (#890)
FIX: Change deprecated normed to density in parameters to hist() (#888)
ENH: Write derivatives metadata (#885)
ENH: Add --pdb option to make debugging easier (#884)

- Python
Published by effigies about 5 years ago

mriqc - 0.16.0

Release Notes

New feature release in 0.16.x series.

This version removes the FSL dependency from the fMRI workflow.

CHANGES

FIX: Skip version cache on read-only filesystems (#862)
FIX: Honor $OMP_NUM_THREADS environment variable (#848)
RF: Simplify comprehensions, using easy-to-read var names (#875)
RF: Free the fMRI workflow from FSL (#842)
CI: Fix up Circle builds (#876)
CI: Update machine images on Circle (#874)

- Python
Published by effigies about 5 years ago

mriqc - 0.15.2

Release Notes

A bugfix release containing mostly maintenance actions and documentation improvements. This version drops Python 3.5. The core of MRIQC has adopted the config-module pattern from fMRIPrep.

With thanks to A. Erramuzpe, @justbennet, U. Tooley, and A. Huffman for contributions.

CHANGES

RF: Adopt config module pattern from fMRIPrep (#837)
MAINT: Clear the clutter of warnings (#838)
MAINT: Drop Python 3.5, simplify linting (#833)
MAINT: Update to latest Ubuntu Xenial tag (#814)
MAINT: Centralize all requirements and versions on setup.cfg (#819)
MAINT: Use recent Python image to build packages in CircleCI (#808)
DOC: Improve AQI (and other IQMs) and boxplot whiskers descriptions (#816)
DOC: Refactor how documentation is built on CircleCI (#818)
DOC: Corrected a couple of typos in --help text (#809)

- Python
Published by oesteban almost 6 years ago

mriqc - 0.15.2rc1

- Python
Published by oesteban over 6 years ago

mriqc - 0.15.1

Release Notes

A maintenance patch release updating PyBIDS.

CHANGES

FIX: FileNotFoundError when MELODIC (--ica) does not converge (#800) @oesteban
MAINT: Migrate MRIQC to a setup.cfg style of installation (#799) @oesteban
MAINT: Use PyBIDS 0.9.2+ via niworkflows PR (#796) @effigies

- Python
Published by oesteban over 6 years ago

mriqc - 0.15.0.post1

Forcing a push to Zenodo.

- Python
Published by oesteban almost 7 years ago

mriqc - 0.15.0

Release Notes

A long overdue update, pinning updated versions of TemplateFlow <https://doi.org/10.5281/zenodo.2583289>__ and Niworkflows <https://github.com/poldracklab/niworkflows>__. With thanks to @garciadias for contributions.

CHANGES

ENH: Revision of QI2 (#606) @oesteban
FIX: Set matplotlib backend early (#759) @oesteban
FIX: Niworkflows pin <0.5 (#766) @oesteban
DOC: Update BIDS validation link. (#764) @garciadias
DOC: Add data sharing agreement (#765) @oesteban
FIX: Catch uncaught exception in WebAPI upload. (#774) @rwblair
FIX/DOC: Append new line after dashes in mriqc_run help text (#777) @rwblair
ENH: Use TemplateFlow and niworkflows-0.8.x (#782) @oesteban
FIX: Correctly set WebAPI rating endpoint in BOLD reports. (#785) @oesteban
FIX: Correctly process values of rating widget (#787) @oesteban

- Python
Published by oesteban almost 7 years ago

mriqc - 0.14.2

Release Notes

Hotfix release

CHANGES

[FIX] Preempt pandas resolving Path objects (#746) @oesteban
[FIX] Codacy issues (#745) @oesteban

- Python
Published by release-drafter[bot] over 7 years ago

mriqc - 0.14.1

Release Notes

A hotfix release, since the outputs of multi-session datasets were not correctly structured. Includes a new toggle button to close off and bring back on the rating widget.

CHANGES

[FIX] Calculate relative path with sessions (#742) @oesteban
[ENH] Add a toggle button to rating widget (#743) @oesteban

- Python
Published by release-drafter[bot] over 7 years ago

mriqc - 0.14.0

Release Notes

A new release with a totally new rating widget. Now, it uploads the ratings to the Web API and also allows to download a JSON file with the manual rating to be stored in disk.

CHANGES

[ENH] New feedback widget (#740) @oesteban

- Python
Published by release-drafter[bot] over 7 years ago

mriqc - 0.13.1

Release Notes

A hotfix release improving the individual reports

CHANGES

[ENH,FIX] Updates to individual reports, fix table after rating (#739) @oesteban

- Python
Published by release-drafter[bot] over 7 years ago

mriqc - 0.13.0

Release Notes

A deep revision of the code, including some fixes to address the memory issues. The outputs have been re-organized in way closer to the current BIDS-Derivatives draft. Additionally, some low-hanging-fruit fixes have also been included.

CHANGES

[MAINT] Overdue refactor (#736) @oesteban
- [FIX] Reorganize outputs (closes #396)
- [ENH] Memory usage - lessons learned with FMRIPREP (#703)
- [FIX] Cannot allocate memory (v 0.9.4) (closes #536)
- [FIX] Drop inoperative --report-dir flag (#550)
- [FIX] Drop misleading WARNING of the group-level execution (#714)
- [FIX] Expand usernames on input paths (#721)
- [MAINT] More robust naming of derivatives (related to #661)
[FIX] Do not fail with spurious 4th dimension on T1w (#738) @oesteban
[ENH] Move on to .tsv files (#737) @oesteban

- Python
Published by release-drafter[bot] over 7 years ago

mriqc - 0.12.1

Release notes

A hotfix release to enable the BIDS filtering arguments (--session-id, --task-id, --run-id).

CHANGES

[FIX] BIDSLayout queries (#735)

- Python
Published by oesteban over 7 years ago

mriqc - 0.12.0

Release Notes

The most relevant increment of this release is migrating back to a standalone nipype installation, of the latest version (1.1.1).

CHANGES

[FIX] Reduce tSNR memory requirements (#712)
[DOC] Fix typos in IQM documentation (#725)
[PIN] Update MRIQC WebAPI version (#734)
[BUG] Fix missing library in singularity images (#733)
[PIN] nipype 1.1.1, niworkflows (#726)

- Python
Published by oesteban over 7 years ago

mriqc - 0.11.0

Release Notes

This release restores drop-in compatibility with Nipype.

CHANGES

RF: Resume external nipype dependency (#715)

- Python
Published by oesteban over 7 years ago

mriqc - 0.10.6

Hotfix to an error submitting rating feedback

- Python
Published by oesteban almost 8 years ago

mriqc - 0.10.5

Release Notes

With big thanks to @rwblair for his implementation of the report feedback, to be presented in ISMRM 2018 (https://www.biorxiv.org/content/early/2017/11/09/216671).

With this new feature, mriqc-ers will be able to submit their own annotations to the MRIQC-Web API. Crowdsourcing these ratings will probably enable to push the accuracy of automated prediction software (such as MRIQC) by enabling training on larger, heterogeneous, multi-site samples.

CHANGES

[ENH] Report feedback (#659)

- Python
Published by oesteban almost 8 years ago

mriqc - 0.10.4

CHANGES

[ENH] Various improvements to reports (#708)
[MAINT] Style revision (#704)
[PIN] pybids 0.5 (#700)
[ENH] Increase FAST memory limits (#702)

- Python
Published by oesteban almost 8 years ago

mriqc - 0.10.3

Release notes

Update niworkflows and allow T2w metrics uploads to the Web-API.

CHANGES

With thanks to @jokedurnez for contributions.

[ENH] Enable T2w metrics uploads (#696)
[PIN] Updating niworkflows (#698)
[DOC] Option -o is outdated for classifier (#697)

- Python
Published by oesteban about 8 years ago

mriqc - 0.10.2

Release notes

Hotfix for a problem with xform headers of nifti files

CHANGES

[ENH] Add warning about mounting relative paths (#690)
[FIX] Sanitize inputs (#687)
[DOC] Fix documentation to use --version instead of -v (#688)

- Python
Published by oesteban about 8 years ago

mriqc - 0.10.1

[FIX] Fixed a bug in reading outputs of 3dFWHMx (#678)

- Python
Published by chrisgorgo about 8 years ago

mriqc - 0.10.0

CHANGES

[ENH] Update AFNI to the current latest version (#669).
[ENH] Update pybids (#668)

- Python
Published by oesteban over 8 years ago

mriqc - 0.9.10

With thanks to @justbennet for contributions

CHANGES

[FIX] Update niworkflows (#656)
[ENH] Recursively set read/Xecute permission for miniconda (#650)

- Python
Published by oesteban over 8 years ago

mriqc - 0.9.9

With thanks to @justbennet for contributions on containerization.

[ENH] Update nipype to the latest dev version, which includes many improvements and bugfixes.
[ENH] Use new resource monitoring of nipype.

- Python
Published by oesteban over 8 years ago

mriqc - 0.9.8

With thanks to Jan Varada (@jvarada) for the session/run filtering.

CHANGES

[ENH] Report recall in cross-validation (requested by reviewer) (#633)
[ENH] Hotfixes to 0.9.7 (#635)
[FIX] Implement filters for session, run and task of BIDS input (#612)

- Python
Published by oesteban over 8 years ago

mriqc - 0.9.7

CHANGES

[ENH] Clip outliers in FD and SPIKES group plots (#593)
[ENH] Second revision of the classifier (#555):
- Set matplotlib plugin to agg in docker image
- Migrate scalings to sklearn pipelining system
- Add Satra's feature selection for RFC (with thanks to S. Ghosh for his suggestion)
- Make model selection compatible with sklearn Pipeline
- Multiclass classification
- Add feature selection filter based on Sites prediction (requires pinning to development sklearn-0.19)
- Add RobustLeavePGroupsOut, replace RobustGridSearchCV with the standard GridSearchCV of sklearn.
- Choice between RepeatedStratifiedKFold and RobustLeavePGroupsOut in mriqc_clf
- Write cross-validation results to an .npz file.
[ENH] First revision of the classifier (#553):
- Add the possibility of changing the scorer function.
- Unifize labels for raters in data tables (to rater_1)
- Add the possibility of setting a custom decision threshold
- Write the probabilities in the prediction file
- Revised mriqc_clf processing flow
- Revised labels file for ds030.
- Add IQMs for ABIDE and DS030 calculated with MRIQC 0.9.6.
ANNOUNCEMENT: Dropped support for Python<=3.4
WARNING (#596): We have changed the default number of threads for ANTs. Using parallelism with ANTs causes numerical instability on the calculated measures. The most sensitive metrics to this problem are the kurtosis calculations on the intensities of regions and qi_2.

- Python
Published by oesteban over 8 years ago

mriqc - 0.9.6

MRIQC 0.9.6 incorporates the new MRIQCWebAPI and bugfixes.

CHANGES

[ENH] Finished setting up MRIQC Web API
[ENH] Better error message when --participant_label is set (#542)
[FIX] Allow --load-classifier option to be empty in mriqc_clf (#544)
[FIX] Borked bias estimation derived from Conform (#541)
[ENH] Test against web API 0.3.2 (#540)
[ENH] Change the default Web API address (#539)
[ENH] MRIQCWebAPI: hash fields that may have PI (#538)
[ENH] Added token authorization to MRIQCWebAPI client (#535)
[FIX] Do not mask and antsAffineInitializer twice (#534)
[FIX] Datasets where air (hat) mask is empty (#533)
[ENH] Integration testing for MRIQCWebAPI (#520)
[ENH] Use AFNI to calculate gcor (#531)
[ENH] Refactor derivatives (#530)
[ENH] New bold-IQM: dummy_trs (non-stady state volumes) (#524)
[FIX] Order of BIDS components in IQMs CSV table (#525)
[ENH] Improved logging of mriqc_run (#526)

- Python
Published by oesteban over 8 years ago

mriqc - 0.9.5

A new release exploring the new intensity normalization.

Changes

[ENH] Refactored structural metrics calculation (#513)
[ENH] Calculate rotation mask (#515)
[ENH] Intensity harmonization in the anatomical workflow (#510)
[ENH] Set N4BiasFieldCorrection number of threads (#506)
[ENH] Convert FWHM in pixel units (#503)
[ENH] Add MRIQC client for feature crowdsourcing (#464)
[DOC] Fix functional feature labels in documentation (docs_only) (#507)
[FIX] New implementation for the rPVE feature (normalization, left-tail values) (#505)
[ENH] Parse BIDS selectors (run, task, etc.), improve CLI (#504)

- Python
Published by oesteban almost 9 years ago

mriqc - 0.9.4

MRIQC 0.9.4 includes some bugfixes, and several maintenance patches (especially in continuous testing). Finally, a great speedup has been introduced in the new spatial normalization of T1w images (at the cost of accuracy).

Changes

ANNOUNCEMENT: Dropped Python 2 support
[ENH] Use versioneer to handle versions (#500)
[ENH] Speed up spatial normalization (#495)
[ENH] Resampling of hat mask and TPMs with linear interp (#498)
[TST] Build documentation in CircleCI (#484)
[ENH] Use full-resolution T1w images from ABIDE (#486)
[TST] Parallelize tests (#493)
[TST] Binding /etc/localtime stopped working in docker 1.9.1 (#492)
[TST] Downgrade docker to 1.9.1 in circle (build_only) (#491)
[TST] Check for changes in intermediate nifti files (#485)
[FIX] Erroneous flag --n_proc in CircleCI (#490)
[ENH] Add build_only tag to circle builds (#488)
[ENH] Update Dockerfile (#482)
[FIX] Ignore --profile flag with Linear plugin (#483)
[DOC] Deep revision of the documentation (#479)
[ENH] Minor improvements: SpatialNormalization and segmentation (#472)
[ENH] Fixed typo for neurodebian install via apt-get (#478)
[ENH] Updating fs2gif script (#465)
[ENH] RF: Use niworkflows.interface.SimpleInterface (#468)
[ENH] Add reproducibility of metrics tracking (#466)

- Python
Published by oesteban almost 9 years ago

mriqc - 0.9.3

[ENH] Refactor of the Dockerfile to improve transparency, reduce size, and enable injecting code in Singularity (#457)
[ENH] Make more the memory consumption estimates of each processing step more conservative to improve robustness (#456)
[FIX] Minor documentation cleanups (#461)

- Python
Published by chrisgorgo almost 9 years ago

mriqc - 0.9.2

[ENH] Optional ICA reports for identifying spatiotemporal artifacts (#412)
[ENH] Add --profile flag (#435)
[ENH] Crashfiles are saved in plain text to improve portability (#434)
[FIX] Fixes EPI mask erosion (#442)
[ENH] Make FSL and AFNI motion correction more comparable by using the same scheme for defining the reference image (#444)
[FIX] Temporarily disabling T1w quality classifier until it can be retrained on new measures (#447)

- Python
Published by chrisgorgo almost 9 years ago

mriqc - 0.9.1

[ENH] Add mriqc version and input image hash to IQMs json file (#432)
[FIX] Affine and warp transforms are now applied in the correct order (#431)

- Python
Published by chrisgorgo almost 9 years ago

mriqc - v0.9.0 revision 1

A stable MRIQC release, fixing the most prominent bugs and issues found. This is a transient version before 1.0.0 is released.

CHANGELOG

[FIX] BOLD reports clipped IQMs after spikes_num (#425)
[FIX] Unicode error writing group reports (#424)
[FIX] Respect Nifi header in fMRI conform node (#415)
[DOC] Deep revision of documentation (#411, #416)
[ENH] Added sphinx extension to plot workflow graphs (#411)
[FIX] Removed repeated bias correction on anatomical workflows (#410)
[FIX] Race condition in bold workflow when using shared workdir (#409)
[FIX] Tests (#408, #407, #405)
[FIX] Remove CDN for group level reports (#406)
[FIX] Unused connection, matplotlib segfault (#403, #402)
[ENH] Skip SpikeFFT detector by default (#400)
[ENH] Use float32 (#399)
[ENH] Spike finder performance improvoments (#398)
[ENH] Basic T2w workflow (#394)
[ENH] Re-enable 3dvolreg (#390)
[ENH] Add T1w classifier (#389)

- Python
Published by oesteban almost 9 years ago

mriqc - v0.9.0

A stable MRIQC release, fixing the most prominent bugs and issues found. This is a transient version before 1.0.0 is released.

CHANGELOG

[ENH] Improve group level command line, with more informative output when no IQMs are found for a modality (#372)
[ENH] Make group reports self-contained (#333)
[FIX] New mosaics, based on old ones (#361, #360, #334)
[FIX] Require numpy>=1.12 to avoid casting problems (#356)
[FIX] Add support for acq and rec tags of BIDS (#346)
[DOC] Documentation updates (#350)
[FIX] pybids compatibility "No scans were found" (#340, #347, #342)
[ENH] Rewrite PYTHONPATH in docker/singularity images (#345)
[ENH] Move metadata onto the bottom of the individual reports (#332)
[ENH] Don't include MNI registration report unles --verbose-reports is used (#362)

- Python
Published by oesteban about 9 years ago

mriqc - v0.9.0 Release Candidate 2

- Python
Published by oesteban about 9 years ago

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