==========================
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)