21.0.0 (December 14, 2021)
==========================
A new series is finally here!
Some highlights of this version's new features include a substantial rework of fMRIPrep's
susceptibility distortion correction (including the addition of FSL's `topup` as the new
default PEPOLAR correction technique), improved flexibility for multiecho scans, and
dependency version upgrades within the Docker environment.
.. note::
To follow BIDS Derivatives more closely, *fMRIPrep*'s default output layout has changed.
To enable the legacy layout, use the `--output-layout legacy` flag.
For more information, please see https://fmriprep.org/en/latest/outputs.html#layout
.. 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.
* DOC: Remove mention to ``epidewarp.fsl`` from ``NOTICE`` (#2629)
* DOC: Update description of output layout, add discussion of legacy mode (#2646)
* DOC: ME | Add missing output to documentation, improve boilerplate (#2608)
* DOC: Add --index-metadata to `pybids layout` faq (#2546)
* DOC: Add warning about slice timing correction in output documentation. (#2502)
* 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)
* DOCKER: Shrink Docker image size (#2551)
* DOCKER: Strip ABI tag from libQt5Core.so.5 to prevent Singularity failures (#2535)
* ENH: Make bids the default output layout option (#2555)
* ENH: Mask multi-echo data with reference mask instead of echo-specific masks (#2349)
* ENH: Replace initial FLIRT with mri_coreg, use -basescale 1 for FLIRT-BBR (#2625)
* 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)
* ENH: Tedana-friendly ME derivatives (#2575)
* ENH: Better integration of *SDCFlows*' unwarping (#2576)
* ENH: Refactor workflow to adopt *SDCFlows*' new correction workflow (#2547)
* FIX: Threshold boldref resampled values to be non-negative (#2630)
* FIX: Restore SyN-SDC (#2530)
* FIX: Confusing I/O field ``bold_mask`` in bold-to-bold resampling workflow (#2611)
* FIX: ME | Revise SDC compute graph (#2610)
* FIX: Propagate the SDC warp to resampling node also with ME (#2609)
* FIX: Optimize build job on CircleCI (#2605)
* FIX: Minor multiecho issues (#2574)
* FIX: Missing numpy import (#2533)
* 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: Conform fast-track outputs to BIDS ordering (#2663)
* MAINT: Reduce redundant processing of ds005 (#2649)
* MAINT: Finalize the work we started with the refactor of the Docker image (#2601)
* MAINT: Run full workflows on tags (#2593)
* MAINT: Stage Python environment of Docker image from nipreps/miniconda (#2581)
* MAINT: Stop NeuroDebian dependency in Dockerfile (#2578)
* MAINT: Run pytest through GitHub actions (#2529)
* 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)
* RF/FIX: Iterate over echo indices, not filenames, simplifying iteration logic (#2651)