Tags: mky27/mriqc
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23.1.1 Release Notes ------------- A long-overdue hotfix release addressing many bugs generated during the development of the new dMRI workflows, and some relating to improvements of the handling of multi-echo fMRI. The release also include one year-worth of maintenance actions and a general code cleanup with *Ruff*. CHANGES ------- * FIX: Missing conection to head-motion estimation node in DWI workflow by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1207 <https://github.com/nipreps/mriqc/pull/1207>`__ * FIX: Revise porting to ``Loader`` by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1201 <https://github.com/nipreps/mriqc/pull/1201>`__ * FIX: Revise the last two sloppy merges by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1200 <https://github.com/nipreps/mriqc/pull/1200>`__ * FIX: Move from ``pkg_resources`` to ``niworkflows.data.Loader`` by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1199 <https://github.com/nipreps/mriqc/pull/1199>`__ * FIX: DIPY not listed as a dependency by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1197 <https://github.com/nipreps/mriqc/pull/1197>`__ * FIX: Include ``dwidenoise`` within Docker image by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1196 <https://github.com/nipreps/mriqc/pull/1196>`__ * FIX: Copy name attribute of ``dataset_description.json`` from input dataset by `@celprov <https://github.com/@celprov>`__ in `nipreps#1187 <https://github.com/nipreps/mriqc/pull/1187>`__ * FIX: Remove FD as an ``iterfield`` in ``MapNode`` causing crash with ME-BOLD by `@celprov <https://github.com/@celprov>`__ in `nipreps#1179 <https://github.com/nipreps/mriqc/pull/1179>`__ * FIX: Incorrect plugin metadata passed to *Report Assembler* by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1188 <https://github.com/nipreps/mriqc/pull/1188>`__ * FIX: Temporary fix of the missing ``"dwi"`` key by `@celprov <https://github.com/@celprov>`__ in `nipreps#1174 <https://github.com/nipreps/mriqc/pull/1174>`__ * FIX: Rearrange multi-echo report by `@celprov <https://github.com/@celprov>`__ in `nipreps#1164 <https://github.com/nipreps/mriqc/pull/1164>`__ * FIX: Typo in ``inputnode`` field in dMRI masking workflow by `@celprov <https://github.com/@celprov>`__ in `nipreps#1165 <https://github.com/nipreps/mriqc/pull/1165>`__ * FIX: Bug in group level workflow by `@celprov <https://github.com/@celprov>`__ in `nipreps#1148 <https://github.com/nipreps/mriqc/pull/1148>`__ * FIX: Bugs in DWI workflow by `@celprov <https://github.com/@celprov>`__ in `nipreps#1147 <https://github.com/nipreps/mriqc/pull/1147>`__ * FIX: Use simpler DWI reference workflow by `@yibeichan <https://github.com/@yibeichan>`__ in `nipreps#1145 <https://github.com/nipreps/mriqc/pull/1145>`__ * FIX: Drop deprecated *Networkx*'s API by `@celprov <https://github.com/@celprov>`__ in `nipreps#1137 <https://github.com/nipreps/mriqc/pull/1137>`__ * FIX: Replace ``np.float`` by ``np.float64`` by `@celprov <https://github.com/@celprov>`__ in `nipreps#1140 <https://github.com/nipreps/mriqc/pull/1140>`__ * ENH: Improved logging and optimize early checkpoint on subjects by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1198 <https://github.com/nipreps/mriqc/pull/1198>`__ * ENH: Store confound timeseries data by `@psadil <https://github.com/@psadil>`__ in `nipreps#1166 <https://github.com/nipreps/mriqc/pull/1166>`__ * ENH: Large overhaul of the functional workflow w/focus on ME-EPI by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1155 <https://github.com/nipreps/mriqc/pull/1155>`__ * ENH: Implement BIDS filters file and drop legacy BIDS querying by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1154 <https://github.com/nipreps/mriqc/pull/1154>`__ * ENH: Swap background and zoomed-in visualizations in anatomical reports by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1151 <https://github.com/nipreps/mriqc/pull/1151>`__ * MAINT: Test on *Python* 3.12 by `@DimitriPapadopoulos <https://github.com/@DimitriPapadopoulos>`__ in `nipreps#1156 <https://github.com/nipreps/mriqc/pull/1156>`__ * MAINT: Disable flaky T1w test on CircleCI by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1202 <https://github.com/nipreps/mriqc/pull/1202>`__ * MAINT: Overhaul of the ``Dockerfile`` by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1195 <https://github.com/nipreps/mriqc/pull/1195>`__ * MAINT: Revise package's extra dependencies by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1194 <https://github.com/nipreps/mriqc/pull/1194>`__ * MAINT: Clean up some ``setuptools_scm`` remnants by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1193 <https://github.com/nipreps/mriqc/pull/1193>`__ * MAINT: Load ``FMRISummary`` from *NiReports* rather than *NiWorkflows* by `@celprov <https://github.com/@celprov>`__ in `nipreps#1167 <https://github.com/nipreps/mriqc/pull/1167>`__ * MAINT: Update to latest *migas*' API by `@mgxd <https://github.com/@mgxd>`__ in `nipreps#1160 <https://github.com/nipreps/mriqc/pull/1160>`__ * MAINT: Update bold to large resource class in ``config.yml`` by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1158 <https://github.com/nipreps/mriqc/pull/1158>`__ * MAINT: Refresh cached intermediate results by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1143 <https://github.com/nipreps/mriqc/pull/1143>`__ * MAINT: Simplify GitHub actions checks and update action versions by `@effigies <https://github.com/@effigies>`__ in `nipreps#1141 <https://github.com/nipreps/mriqc/pull/1141>`__ * MAINT: Python 3.11 is supported by `@DimitriPapadopoulos <https://github.com/@DimitriPapadopoulos>`__ in `nipreps#1123 <https://github.com/nipreps/mriqc/pull/1123>`__ * MAINT: Apply suggestions from pyupgrade by `@DimitriPapadopoulos <https://github.com/@DimitriPapadopoulos>`__ in `nipreps#1124 <https://github.com/nipreps/mriqc/pull/1124>`__ * DOC: Update *Sphinx* pinned version to 5 by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1192 <https://github.com/nipreps/mriqc/pull/1192>`__ * DOC: http:// → https:// by `@DimitriPapadopoulos <https://github.com/@DimitriPapadopoulos>`__ in `nipreps#1126 <https://github.com/nipreps/mriqc/pull/1126>`__ * DOC: Add info on the *FreeSurfer* requirement for bare install to address nipreps#1034 by `@neurorepro <https://github.com/@neurorepro>`__ in `nipreps#1130 <https://github.com/nipreps/mriqc/pull/1130>`__ * STY: Add *Ruff* config and fix all warnings and errors by `@oesteban <https://github.com/@oesteban>`__ in `nipreps#1203 <https://github.com/nipreps/mriqc/pull/1203>`__ * STY: Remove extraneous parentheses by `@DimitriPapadopoulos <https://github.com/@DimitriPapadopoulos>`__ in `nipreps#1186 <https://github.com/nipreps/mriqc/pull/1186>`__ * STY: Apply a few refurb suggestions by `@DimitriPapadopoulos <https://github.com/@DimitriPapadopoulos>`__ in `nipreps#1162 <https://github.com/nipreps/mriqc/pull/1162>`__ * STY: Fix typo found by codespell by `@DimitriPapadopoulos <https://github.com/@DimitriPapadopoulos>`__ in `nipreps#1161 <https://github.com/nipreps/mriqc/pull/1161>`__
23.1.0 Release Notes ------------- A new minor release featuring the new individual reports built with the new *NiReports* VRS (visual reports system). This means *MRIQC* now uses the same package *fMRIPrep* uses for generating its reports. In addition to that, this new release also features *Beta* support for diffusion MRI (dMRI). CHANGES ------- * FIX: Better handling of BIDS cached indexation (nipreps#1121) * FIX: Make doctest of ``NumberOfShells`` more reliable (nipreps#1122) * FIX: Add protection for NaNs and INFs when calculating QI2 (nipreps#1112) * FIX: ``PlotMosaic`` expects lists, not tuples (nipreps#1111) * FIX: BIDS database directory handling (nipreps#1110) * FIX: Remove unused dipy import in the functional interfaces (nipreps#1109) * FIX: Refine the head mask after removal of FSL BET (nipreps#1107) * FIX: Inform *SynthStrip* about the desired intraop threads (nipreps#1101) * FIX: Test broken by nipreps#1098 (nipreps#1100) * FIX: Separate report bootstrap files (anat vs. func) (nipreps#1098) * FIX: Propagate logging level to subprocesses (nipreps#1030) * ENH: Incorporate new NiReports' DWI heatmaps (nipreps#1119) * ENH: More compact of shell-wise summary statistic maps (avg/std) (nipreps#1116) * ENH: Add a basic DTI fitting into the diffusion workflow (nipreps#1115) * ENH: MRIQC for DWI (nipreps#1113) * ENH: Culminate dropping FSL as a dependency (nipreps#1108) * ENH: Replace FSL FAST with ANTs Atropos for brain tissue segmentation (nipreps#1099) * ENH: Drop FSL MELODIC (without alternative) (nipreps#1106) * ENH: Drop FSL BET to estimate the "outskin" (head) mask (nipreps#1105) * ENH: Drop utilization of "head" mask from template (nipreps#1104) * ENH: Move templates' probsegs into individual at normalization (nipreps#1103) * ENH: Improving the resource monitor -- infer PID from process name (nipreps#1049) (nipreps#1049) * ENH: Refactor reports system to use *NiReports* and the general VRS (nipreps#1085) * MAINT: Move codespell configuration to ``pyproject.toml`` (nipreps#1097) * MAINT: Update deprecated ``nibabel.spatialimage.get_data()`` calls (nipreps#1096)
23.1.0rc0 A new minor release featuring the new individual reports built with the new *NiReports* VRS (visual reports system). This means *MRIQC* now uses the same package *fMRIPrep* uses for generating its reports. * FIX: Propagate logging level to subprocesses (nipreps#1030) * ENH: Refactor reports system to use *NiReports* and the general VRS (nipreps#1085) * MAINT: Update deprecated ``nibabel.spatialimage.get_data()`` calls (nipreps#1096)
23.0.1 (March 24, 2023) A hotfix release resolving a reggression introduced with the new optimized indexing. * FIX: Underspecified regex sets ``BIDSLayout`` to ignore data with sesions (nipreps#1094) * FIX: Input data has incompatible dimensionality (plotting ICA) (nipreps#1082) * ENH: Optimize metadata gathering reusing ``BIDSLayout`` db (nipreps#1084) * DOC : update anatomical example report in documentation (nipreps#1088) * MAINT: Drop old ``mriqc_plot`` script (nipreps#1091)
23.0.0 The new 23.0.x series include several prominent changes. Visualization has been migrated from *MRIQC* and *niworkflows* over to the new *NiReports* project. This series include a major bugfix with **the optimization of the indexing** of the input BIDS folder, which was taking large times with sizeable datasets. Telemetry has also been incorporated with *migas*. These new series also involve maintenance housekeeping, and includes some relevant bugfixes. New contributors ---------------- * `@arokem <https://github.com/arokem>`__ made their first contribution in `nipreps#1040 <https://github.com/nipreps/mriqc/pull/1040>`__ * `@yarikoptic <https://github.com/yarikoptic>`__ made their first contribution in `nipreps#1057 <https://github.com/nipreps/mriqc/pull/1057>`__ * `@esavary <https://github.com/esavary>`__ made their first contribution in `nipreps#1047 <https://github.com/nipreps/mriqc/pull/1047>`__ CHANGES ------- **Full Changelog**: nipreps/mriqc@22.0.6...23.0.0 * FIX: Send metadata extraction to workers (functional workflow) (nipreps#1081) * FIX: Plot coronal as main plain for mosaic of rodent images (nipreps#1027) * FIX: Address non-empty take from empty axes (anatomical IQMs) (nipreps#1077) * FIX: Uniformize building workflow message (anat vs. func) (nipreps#1072) * FIX: Move telemetry atexit into entrypoint func (nipreps#1067) * FIX: Preempt PyBIDS to spend time indexing non-BIDS folders (nipreps#1050) * FIX: Update T1w metrics (nipreps#1063) * FIX: Resource monitor would not ever start tracking (nipreps#1051) * ENH: Add DataLad getter to inputs of functional workflows (nipreps#1071) * ENH: Add migas telemetry (nipreps#1036) * ENH: Add codespell automation: config, action, and typos fixed (nipreps#1057) * MAINT: Update *NiReports* calls to upcoming interfaces API (nipreps#1078) * MAINT: Pacify codespell (nipreps#1080) * MAINT: Conclude porting of reportlets into *NiReports* (nipreps#1068) * MAINT: Migrate to hatchling (nipreps#1070) * MAINT: Pin PyBIDS 0.15.6 (culminating nipreps#1050) (nipreps#1069) * MAINT: Update niworkflows pin to support newer ANTs releases (nipreps#1047) * MAINT: Fix minor aspects of WebAPI deployment on CircleCI (nipreps#1064) * MAINT: Update CircleCI executor and use built-in docker-compose (nipreps#1061) * MAINT: Rotate CircleCI secrets and setup up org-level context (nipreps#1046) * DOC: Update documentation with the new carpet plot (nipreps#1045) * DOC: Complete the documentation of ``summary_stats()`` (nipreps#1044) * DOC: Fixes a couple of broken links to the *nipype* documentation (nipreps#1040)
22.0.6 Release Notes ------------- A hotfix release partially rolling-back the previous fix nipreps#1025. Thanks everyone for your patience with the excessively rushed release of 22.0.5. CHANGES ------- * FIX: Better fix to the multi-argument ``--participant-label`` issue (nipreps#1026)
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22.0.5 Release Notes ------------- A hotfix release addressing a problem with the argument parser. CHANGES ------- * FIX: Multiple valued ``--participant-label`` wrongly parsed (nipreps#1025)
22.0.4 Release Notes ------------- A hotfix release to ensure smooth operation of datalad within Docker. CHANGES ------- * FIX: Major improvements to new datalad-based interface & perform within containers (nipreps#1024) * ENH: Bump Docker base to latest release (nipreps#1022)
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