20.2.6 (LTS)

Release Notes

Patch release in the 20.2.x LTS series.

This release includes an updated runtime environment for Docker/Singularity users.
This environment includes a newer release of indexed_gzip, fixing CrcErrors previously encountered.

Changes

• CI: Run full workflows on tags (#2593)
• RF: Add extension field to differentiate from upcoming templates (#2613)

20.2.5 (Long-Term Support)

Release Notes

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.

Changes

• FIX: --slice-time-ref option parsing (#2573)
• CI: Add style checks (missing since Travis got throttled) (#2570)
• FIX: Resample aseg with nearest-neighbor interpolation (nipreps/smriprep#268)
• FIX: Revert to FAST for tissue probability maps (nipreps/smriprep#264)

20.2.4 (Long-Term Support)

Release Notes

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.

Changes

• FIX: Avoid unnecessary connections based on branching logic (#2508)
• FIX: Permit missing TR to show PyBIDS error at workflow construction time (#2513)
• [BACKPORT] FIX: Catch FreeSurfer error related to FIPS being enabled (#2490)
• ENH: Use BIDSLayoutIndexer and do not index unnecessary modalities (#2494)
• [BACKPORT] ENH: Slice-timing correction improvements (#2565)

fMRIPrep 21.0.0rc1

Release Notes

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.

Changes

• DOC: Add --index-metadata to pybids layout faq (#2546)
• DOC: Add warning about slice timing correction in output documentation. (#2502)
• ENH: Make bids the default output layout option (#2555)
• ENH: Mask multi-echo data with reference mask instead of echo-specific masks (#2349)
• FIX: Missing numpy import (#2533)
• DOCKER: Shrink Docker image size (#2551)
• DOCKER: Strip ABI tag from libQt5Core.so.5 to prevent Singularity failures (#2535)
• MAINT: Run pytest through GitHub actions (#2529)

fMRIPrep 21.0.0rc0

Release Notes

The first release candidate of a new major version of fMRIPrep is here!
This release includes multiple enhancements, as well as a few bug-fixes, and features a comprehensive overhaul of susceptibility distortion correction (SDC).

Changes

• DOC: Update sample report (#2519)
• DOC: Refactor README and citing information (#2474)
• DOC: Point documentation at SDCFlows and remove SDC section (#2470)\
• DOC: Transfer duplicated documentation to www.nipreps.org (#2469)
• DOC: Better explanation on how spike regressors are generated (#2465)
• DOC: Clarify that res-2 entity does not mean 2mm (#2466)
• DOC: adds --mem metavar (#2378)
• DOC: skull stripping is forced by default (#2345)
• ENH: Add flag for STC reference time and set in all cases (#2520)
• ENH: Use BIDSLayoutIndexer and do not index unnecessary modalities (#2494)
• ENH: Allow users to download templateflow templates to directory (#2482)
• ENH: Detect 3D & too-short BOLD series, warn and skip run's workflow building (#2461)
• ENH: Modernize Dockerfile (#2409) (#2270)
• ENH: Leverage SDCFlows 2.x API (#2392)
• FIX: Avoid eager imports from NiWorkflows causing API breaks (#2495)
• FIX: Split aCompCor into aCompCor, cCompCor, wCompCor (#2523)
• FIX: Avoid unnecessary connections based on branching logic (#2508)
• FIX: Permit missing TR to show PyBIDS error at workflow construction time (#2513)
• FIX: Simplify STC logic for too short BOLD series (#2489)
• FIX: Catch FreeSurfer error related to FIPS being enabled (#2490)
• FIX: DerivativesDataSink nondeterministic checksums fixed with niworkflows=~1.3.4 (#2458)
• FIX: Address dependency incompatibilities by pinning specific packages (#2463)
• FIX: Unprotected import of sentry_sdk, which is not a dependency (#2460)
• FIX: Clarify phase encoding direction, rather than axis (#2302)
• MAINT: Relicense +20.3.x - BSD-3-Clause -> Apache License 2.0 (#2325)
• MAINT: Add missing OASIS30 WM/BS probsegs (#2471)
• MAINT: Update BIDS validator to 1.8.0 (#2443)
• MAINT: Address the problems of a sloppy merge (#2468)
• MAINT: Containers - remove /root/.npm (#2464)
• MAINT: Remove traces of Xenial base (#2459)
• MAINT: Revise CircleCI's cache tags to avoid mixups between builds (#2457)
• MAINT: Back port CircleCI configuration from dev branch (#2456)
• MAINT: Increase minimum tedana version (#2366)
• MAINT: Docker hub has disabled password authentication (#2448)
• MAINT: Add Lea Waller to contributors.json (#2304)
• MAINT: Move away from nearly deprecated images (#2295)
• MAINT: Migrate from poldracklab to nipreps orgs (#2290)
• MAINT: Ease CI packaging tests (#2472)

20.2.3

Release Notes

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.

CHANGES

• FIX: Address the problems of a sloppy merge (#2468)
• FIX: DerivativesDataSink nondeterministic checksums fixed with niworkflows=~1.3.4 (#2458)
• FIX: Address dependency incompatibilities by pinning specific packages (#2463)
• FIX: Unprotected import of sentry_sdk, which is not a dependency (#2460)
• ENH: Detect 3D & too-short BOLD series, warn and skip run's workflow building (#2461)
• DOC: Transfer duplicated documentation to www.nipreps.org (#2469)
• DOC: Better explanation on how spike regressors are generated (#2465)
• DOC: Clarify that res-2 entity does not mean 2mm (#2466)
• MAINT: Containers - remove /root/.npm (#2464)
• MAINT: Back port CircleCI configuration from dev branch (#2456)

20.2.2 (critical bugfix on the 20.2.x LTS series)

Release Notes

Hot-fix release in the 20.2.x LTS series.
Addressing a bug on fMRIPrep's resampling to standard spaces (#2444).
In addition, some other relevant bug fixes and performance improvements are built into this patch.

CHANGES

• FIX: Feed NiTransforms with LTAs of type RAS2RAS (#2444)
• FIX: Add some clarity to BrokenProcessPool failures (#2436)
• FIX: Fall-back to initializing workflow in main process (#2435)
• FIX: Raise informative error when duplicate subworkflows are added (#2434)
• FIX: Non-existing path or JSON syntax error for --bids-filter-file should raise on error (#2331)
• FIX: Ignore SBRef files if --ignore sbref is passed (#2370)
• ENH: Relax requirement for PyBIDS databases to exist (#2429)
• ENH: Improve _get_series_len performance (#2406)
• ENH: Set and track NumPy's random seed (#2400)
• DOC: Skull-stripping is forced by default (#2430)
• MAINT: Pin nilearn==0.6.2 (#2427)
• MAINT: Pin tedana==0.0.9a1 for LTS branch (#2403)
• MAINT: Failing CI (#2401)

20.1.4 (critical bugfix on the 20.1.x series)

Release Notes

Hotfix release addressing a bug on fMRIPrep's resampling to standard spaces.
This release also includes some maintenance changes handling old versions of software.

CHANGES

• FIX: Feed NiTransforms with LTAs of type RAS2RAS (#2444)
• MAINT: Pin svgutils==0.3.1 for the 20.1.x series (#2450)
• MAINT: Keep pip and setuptools with support for Python 3.5 (#2449)
• MAINT: Some dependencies cannot be left unpinned (#2446)

20.2.1 (Long-Term Support)

Release Notes

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. This layout will likely become the default in future release series.

Changes

• ENH: Output TaskName and timing metadata for all resampled BOLD series (#2320)
• ENH: Add --output-layout CLI option to enable BIDS (YODA) mode (#2303)
• ENH: Add Docker authentication to increase pull rate limit (#2316)
• FIX: Specify logger for warning (#2298)

20.2.0 (Long-Term Support)

Release Notes

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.

fMRIPrep 20.2 LTS introduces the long-term support program. This LTS version will be kindly steered and maintained by the group of Dr. Basile Pinsard and Prof. Pierre Bellec at CRIUGM, (Université de Montréal). The LTS is planned for a window of 4 years of support (i.e., until September 2024).

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!

CHANGES

• 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 (#2271)
• FIX: Restore --ignore t2w/flair options (#2260)
• FIX: Revise the reproducibility of CompCor masks (#2130)
• FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (#2239)
• FIX: Skip the T1w check if --anat-derivatives is provided. (#2201)
• FIX: Storing --bids-filters within config file (#2177)
• FIX: Revise multi-echo reference generation, permitting using SBRefs too (#1803)
• FIX: FreeSurfer license manipulation & canary
• ENH: Output CompCor masks if --debug compcor is passed (#2248)
• ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (#2223)
• ENH: Reuse config (#2240)
• ENH: Save BOLD-anatomical transforms to derivatives folder (#2233)
• ENH: Leverage BIDSLayout's database_path (#2203)
• ENH: Add --no-tty option to fmriprep-docker.py (#2204)
• ENH: Report number of echoes in BOLD summary. (#2184)
• ENH: Ensure NiPype telemetry is just pinged once (#2168)
• DOC: Add FAQ entry for using pre-indexed layouts (#2256)
• DOC: Update reference in "Refinement of Brain Mask" description (#2215)
• DOC: List TemplateFlow templates that need to be prefetched (#2196)
• DOC: Update references to https://github.com/nipreps (#2191)
• DOC: Pin NiPype with new Sphinx extension syntax (#2092)
• MAINT: Upgrade ANTs to 2.3.3 in Dockerfile (9512086)
• MAINT: Track #2269 and #2269, bug-fixes on the 20.1.x series
• MAINT: Remove derivatives from layout index ignores (#2258)
• MAINT: Track #2252 from 20.1.x series (#2253)
• MAINT: Silence PyBIDS warning by setting extension mode (#2250)
• MAINT: Drop CircleCI docs build (#2247)
• MAINT: Pin latest NiPreps (#2244)
• MAINT: Update setup.cfg (flake8 and pytest) (#2183)
• MAINT: Delete release-drafter (#2169)
• MAINT: Track bug-fix release on the 20.1.x series (#2165)
• MAINT: Remove auto-comment bot (#2166)
• MAINT: Improve the questions on the bug-report template (#2158)