Tags: dlinhardt/fmriprep
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20.2.5 (October 12, 2021) Bug-fix release in the 20.2.x LTS series. This release includes a fix to `--slice-time-ref` parsing. Also, some issues in anatomical processing are resolved, including poorly-interpolated labels in aseg segmentations, and probabilistic segmentations have reverted to FAST. * FIX: --slice-time-ref option parsing (nipreps#2573) * CI: Add style checks (missing since Travis got throttled) (nipreps#2570)
20.2.4 (October 04, 2021) Bug-fix release in the 20.2.x LTS series. This release includes some fixes to minor bugs, and includes enhancements to allow the user to specify a different slice-timing-correction (STC) target. Each BOLD series will contain ``SliceTimingCorrected`` metadata to indicate whether STC was performed. If performed, the ``StartTime`` metadata field will be set to indicate the onset time of the BOLD series. * FIX: Avoid unnecessary connections based on branching logic (nipreps#2508) * FIX: Permit missing TR to show PyBIDS error at workflow construction time (nipreps#2513) * [BACKPORT] FIX: Catch FreeSurfer error related to FIPS being enabled (nipreps#2490) * ENH: Use ``BIDSLayoutIndexer`` and do not index unnecessary modalities (nipreps#2494) * [BACKPORT] ENH: Slice-timing correction improvements (nipreps#2565)
21.0.0rc1 (September 21, 2021) ============================= A new release candidate of the upcoming 21.0.x series. Included are some vital bug fixes, a drastic decrease in Docker image size, and a change in the default output directory structure. * DOC: Add --index-metadata to `pybids layout` faq (nipreps#2546) * DOC: Add warning about slice timing correction in output documentation. (nipreps#2502) * ENH: Make bids the default output layout option (nipreps#2555) * ENH: Mask multi-echo data with reference mask instead of echo-specific masks (nipreps#2349) * FIX: Missing numpy import (nipreps#2533) * DOCKER: Shrink Docker image size (nipreps#2551) * DOCKER: Strip ABI tag from libQt5Core.so.5 to prevent Singularity failures (nipreps#2535) * MAINT: Run pytest through GitHub actions (nipreps#2529)
21.0.0rc0 (September 2, 2021) ============================= The first release candidate for a new major version of fMRIPrep! Changes: * DOC: Update sample report (nipreps#2519) * DOC: Refactor README and citing information (nipreps#2474) * DOC: Point documentation at *SDCFlows* and remove SDC section (nipreps#2470)\ * DOC: Transfer duplicated documentation to www.nipreps.org (nipreps#2469) * DOC: Better explanation on how spike regressors are generated (nipreps#2465) * DOC: Clarify that ``res-2`` entity does not mean 2mm (nipreps#2466) * DOC: adds --mem metavar (nipreps#2378) * DOC: skull stripping is forced by default (nipreps#2345) * ENH: Add flag for STC reference time and set in all cases (nipreps#2520) * ENH: Use ``BIDSLayoutIndexer`` and do not index unnecessary modalities (nipreps#2494) * ENH: Allow users to download templateflow templates to directory (nipreps#2482) * ENH: Detect 3D & too-short BOLD series, warn and skip run's workflow building (nipreps#2461) * ENH: Modernize Dockerfile (nipreps#2409) (nipreps#2270) * ENH: Leverage SDCFlows 2.x API (nipreps#2392) * FIX: Avoid eager imports from *NiWorkflows* causing API breaks (nipreps#2495) * FIX: Split aCompCor into aCompCor, cCompCor, wCompCor (nipreps#2523) * FIX: Avoid unnecessary connections based on branching logic (nipreps#2508) * FIX: Permit missing TR to show PyBIDS error at workflow construction time (nipreps#2513) * FIX: Simplify STC logic for too short BOLD series (nipreps#2489) * FIX: Catch FreeSurfer error related to FIPS being enabled (nipreps#2490) * FIX: ``DerivativesDataSink`` nondeterministic checksums fixed with ``niworkflows=~1.3.4`` (nipreps#2458) * FIX: Address dependency incompatibilities by pinning specific packages (nipreps#2463) * FIX: Unprotected import of ``sentry_sdk``, which is not a dependency (nipreps#2460) * FIX: Clarify phase encoding direction, rather than axis (nipreps#2302) * MAINT: Relicense +20.3.x - BSD-3-Clause -> Apache License 2.0 (nipreps#2325) * MAINT: Add missing OASIS30 WM/BS probsegs (nipreps#2471) * MAINT: Update BIDS validator to 1.8.0 (nipreps#2443) * MAINT: Address the problems of a sloppy merge (nipreps#2468) * MAINT: Containers - remove ``/root/.npm`` (nipreps#2464) * MAINT: Remove traces of Xenial base (nipreps#2459) * MAINT: Revise CircleCI's cache tags to avoid mixups between builds (nipreps#2457) * MAINT: Back port CircleCI configuration from dev branch (nipreps#2456) * MAINT: Increase minimum tedana version (nipreps#2366) * MAINT: Docker hub has disabled password authentication (nipreps#2448) * MAINT: Add Lea Waller to ``contributors.json`` (nipreps#2304) * MAINT: Move away from nearly deprecated images (nipreps#2295) * MAINT: Migrate from poldracklab to nipreps orgs (nipreps#2290) * MAINT: Ease CI packaging tests (nipreps#2472)
20.2.3 Patch release in the 20.2.x LTS series. Addresses minimal problems in some edge-cases, overall improves the documentation and infrastructure. Exercises some maintenance operations addressing problems surfaced when the previous tag 20.2.2 was released. * FIX: Address the problems of a sloppy merge (nipreps#2468) * FIX: ``DerivativesDataSink`` nondeterministic checksums fixed with ``niworkflows=~1.3.4`` (nipreps#2458) * FIX: Address dependency incompatibilities by pinning specific packages (nipreps#2463) * FIX: Unprotected import of ``sentry_sdk``, which is not a dependency (nipreps#2460) * ENH: Detect 3D & too-short BOLD series, warn and skip run's workflow building (nipreps#2461) * DOC: Transfer duplicated documentation to www.nipreps.org (nipreps#2469) * DOC: Better explanation on how spike regressors are generated (nipreps#2465) * DOC: Clarify that ``res-2`` entity does not mean 2mm (nipreps#2466) * MAINT: Containers - remove ``/root/.npm`` (nipreps#2464) * MAINT: Back port CircleCI configuration from dev branch (nipreps#2456)
20.2.2 Hot-fix release in the 20.2.x LTS series. Addressing a bug on *fMRIPrep*'s resampling to standard spaces (nipreps#2444). In addition, some other relevant bug-fixes and performance improvements are built in this patch. * FIX: Feed *NiTransforms* with LTAs of type RAS2RAS (nipreps#2444) * FIX: Add some clarity to ``BrokenProcessPool`` failures (nipreps#2436) * FIX: Fall-back to initializing workflow in main process (nipreps#2435) * FIX: Raise informative error when duplicate subworkflows are added (nipreps#2434) * FIX: Non-existing path or JSON syntax error for ``--bids-filter-file`` should raise on error (nipreps#2331) * FIX: Ignore SBRef files if ``--ignore sbref`` is passed (nipreps#2370) * ENH: Relax requirement for *PyBIDS* databases to exist (nipreps#2429) * ENH: Improve ``_get_series_len`` performance (nipreps#2406) * ENH: Set and track NumPy's random seed (nipreps#2400) * DOC: Skull-stripping is forced by default (nipreps#2430) * MAINT: Pin ``nilearn==0.6.2`` (nipreps#2427) * MAINT: Pin ``tedana==0.0.9a1`` for LTS branch (nipreps#2403) * MAINT: Failing CI (nipreps#2401)
20.1.4 Hotfix release addressing a bug on *fMRIPrep*'s resampling to standard spaces. This release also includes some maintenance changes handling old versions of software. * FIX: Feed *NiTransforms* with LTAs of type RAS2RAS (nipreps#2444) * MAINT: Pin ``svgutils==0.3.1`` for the 20.1.x series (nipreps#2450) * MAINT: Keep pip and setuptools with support for Python 3.5 (nipreps#2449) * MAINT: Some dependencies cannot be left unpinned (nipreps#2446)
20.2.1 (November 06, 2020) Bug-fix release in the 20.2.x LTS series. This release adds missing metadata to GIFTI and CIFTI-2 derivatives and fixes a logging bug affecting a small number of datasets. Additionally the ``--output-layout bids`` flag will now output fMRIPrep derivatives directly into the output directory, nesting FreeSurfer derivatives by default in ``<output>/sourcedata/freesurfer``. This layout allows the output root to be a valid BIDS Derivatives dataset, simplifying data management and provenance tracking with content tracking tools, such as `DataLad <https://handbook.datalad.org/>`__. This layout will likely become the default in future release series. * ENH: Output TaskName and timing metadata for all resampled BOLD series (nipreps#2320) * ENH: Add --output-layout CLI option to enable BIDS (YODA) mode (nipreps#2303) * ENH: Add Docker authentication to increase pull rate limit (nipreps#2316) * FIX: Specify logger for warning (nipreps#2298)
20.2.0 (September 28, 2020) With this third minor release series of 2020, the first *fMRIPrep LTS* (*long-term support*) is finally here! This release contains a number of bug-fixes and enhancements mostly related to easing the maintenance, anticipating patch-release breaking changes to ensure a longstanding LTS, and addressing some run-to-run repeatability problems of the CompCor implementation. Thank you for using *fMRIPrep*! If you encounter any issues with this release, please let us know by posting an issue on our GitHub page! A full list of changes can be found below. * FIX: Pin *NiWorkflows* 1.3.1 and *sMRIPrep* 0.7.0rc2, including bugfix for INU-correction failures (nipreps/niworkflows#567) * FIX: Get missing ``probseg`` file from MNI152NLin2009cAsym (nipreps#2271) * FIX: Restore ``--ignore t2w/flair`` options (nipreps#2260) * FIX: Revise the reproducibility of *CompCor* masks (nipreps#2130) * FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (nipreps#2239) * FIX: Skip the T1w check if ``--anat-derivatives`` is provided. (nipreps#2201) * FIX: Storing ``--bids-filters`` within config file (nipreps#2177) * FIX: Revise multi-echo reference generation, permitting using SBRefs too (nipreps#1803) * FIX: *FreeSurfer* license manipulation & canary * ENH: Output CompCor masks if ``--debug compcor`` is passed (nipreps#2248) * ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (nipreps#2223) * ENH: Reuse config (nipreps#2240) * ENH: Save BOLD-anatomical transforms to derivatives folder (nipreps#2233) * ENH: Leverage BIDSLayout's ``database_path`` (nipreps#2203) * ENH: Add ``--no-tty`` option to ``fmriprep-docker.py`` (nipreps#2204) * ENH: Report number of echoes in BOLD summary. (nipreps#2184) * ENH: Ensure *NiPype* telemetry is just pinged once (nipreps#2168) * DOC: Add FAQ entry for using pre-indexed layouts (nipreps#2256) * DOC: Update reference in "Refinement of Brain Mask" description (nipreps#2215) * DOC: List *TemplateFlow* templates that need to be prefetched (nipreps#2196) * DOC: Update references to https://github.com/nipreps (nipreps#2191) * DOC: Pin *NiPype* with new Sphinx extension syntax (nipreps#2092) * MAINT: Upgrade ANTs to 2.3.3 in ``Dockerfile`` (9512086) * MAINT: Track nipreps#2269 and nipreps#2269, bug-fixes on the 20.1.x series * MAINT: Remove derivatives from layout index ignores (nipreps#2258) * MAINT: Track nipreps#2252 from 20.1.x series (nipreps#2253) * MAINT: Silence *PyBIDS* warning by setting extension mode (nipreps#2250) * MAINT: Drop CircleCI docs build (nipreps#2247) * MAINT: Pin latest *NiPreps* (nipreps#2244) * MAINT: Update ``setup.cfg`` (flake8 and pytest) (nipreps#2183) * MAINT: Delete release-drafter (nipreps#2169) * MAINT: Track bug-fix release on the 20.1.x series (nipreps#2165) * MAINT: Remove auto-comment bot (nipreps#2166) * MAINT: Improve the questions on the bug-report template (nipreps#2158)
20.2.0rc2
With this third minor release series of 2020,
the first *fMRIPrep LTS* (*long-term support*) is finally here!
This release contains a number of bug-fixes and enhancements mostly
related to easing the maintenance, anticipating patch-release breaking
changes to ensure a longstanding LTS, and addressing some run-to-run
repeatability problems of the CompCor implementation.
.. admonition:: Long-Term Support (LTS)
*fMRIPrep* 20.2 LTS introduces the `long-term support program
<https://www.nipreps.org/devs/releases/#long-term-support-series>`__.
This LTS version will be kindly steered and maintained by
the group of Dr. Basile Pinsard and Prof. Pierre Bellec at
`CRIUGM <http://www.criugm.qc.ca/>`__, (Université de Montréal).
The LTS is planned for a window of 4 years of support (i.e., until
September 2024).
.. caution::
As with all minor version increments, working directories
from previous versions **should not be reused**.
Thank you for using *fMRIPrep*!
If you encounter any issues with this release, please let us know
by posting an issue on our GitHub page!
A full list of changes can be found below.
* FIX: Pin *NiWorkflows* 1.3.1 and *sMRIPrep* 0.7.0rc2, including bugfix for INU-correction failures (nipreps/niworkflows#567)
* FIX: Get missing ``probseg`` file from MNI152NLin2009cAsym (nipreps#2271)
* FIX: Restore ``--ignore t2w/flair`` options (nipreps#2260)
* FIX: Revise the reproducibility of *CompCor* masks (nipreps#2130)
* FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (nipreps#2239)
* FIX: Skip the T1w check if ``--anat-derivatives`` is provided. (nipreps#2201)
* FIX: Storing ``--bids-filters`` within config file (nipreps#2177)
* FIX: Revise multi-echo reference generation, permitting using SBRefs too (nipreps#1803)
* FIX: *FreeSurfer* license manipulation & canary
* ENH: Output CompCor masks if ``--debug compcor`` is passed (nipreps#2248)
* ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (nipreps#2223)
* ENH: Reuse config (nipreps#2240)
* ENH: Save BOLD-anatomical transforms to derivatives folder (nipreps#2233)
* ENH: Leverage BIDSLayout's ``database_path`` (nipreps#2203)
* ENH: Add ``--no-tty`` option to ``fmriprep-docker.py`` (nipreps#2204)
* ENH: Report number of echoes in BOLD summary. (nipreps#2184)
* ENH: Ensure *NiPype* telemetry is just pinged once (nipreps#2168)
* DOC: Add FAQ entry for using pre-indexed layouts (nipreps#2256)
* DOC: Update reference in "Refinement of Brain Mask" description (nipreps#2215)
* DOC: List *TemplateFlow* templates that need to be prefetched (nipreps#2196)
* DOC: Update references to https://github.com/nipreps (nipreps#2191)
* DOC: Pin *NiPype* with new Sphinx extension syntax (nipreps#2092)
* MAINT: Upgrade ANTs to 2.3.3 in ``Dockerfile`` (9512086)
* MAINT: Track nipreps#2269 and nipreps#2269, bug-fixes on the 20.1.x series
* MAINT: Remove derivatives from layout index ignores (nipreps#2258)
* MAINT: Track nipreps#2252 from 20.1.x series (nipreps#2253)
* MAINT: Silence *PyBIDS* warning by setting extension mode (nipreps#2250)
* MAINT: Drop CircleCI docs build (nipreps#2247)
* MAINT: Pin latest *NiPreps* (nipreps#2244)
* MAINT: Update ``setup.cfg`` (flake8 and pytest) (nipreps#2183)
* MAINT: Delete release-drafter (nipreps#2169)
* MAINT: Track bug-fix release on the 20.1.x series (nipreps#2165)
* MAINT: Remove auto-comment bot (nipreps#2166)
* MAINT: Improve the questions on the bug-report template (nipreps#2158)
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