Fmriprep

=======================
Bug-fix release in the 21.0.x series.

This release includes a few bug-fixes for susceptibility distortion correction (SDC) and multi-echo (ME).
A few notable fixes include:
- Added tolerance for affine precision differences when using EPI fieldmaps.
- Removed hang-ups when reusing anatomical derivatives with ME data.
- Increased BOLD masking workflow robustness.

A full list of changes can be found below:

* DOCKER: Update multiarch deb package link (2758)
* ENH: Add affine_tolerance flag to MergeSeries (nipreps/niworkflows706)
* FIX: Initialize BIDS layout after cleaning working directory (2741)
* FIX: Avoid double unwarping during resampling of processed multi-echo data (2730)
* FIX: Account for potential lists of lists in multi-echo cases (nipreps/niworkflows719)
* FIX: Improve reliability of BOLD masking workflow (nipreps/niworkflows712)
* FIX: Relax tolerance for different affines when concatenating blips (nipreps/sdcflows265)

=========================
Bug-fix release in the 21.0.x series.

This release re-enables reverse-PE EPI fieldmaps, i.e. EPIs acquired with the
opposite phase-encoding direction to a BOLD series.
Additionally, the ``--use-syn-sdc`` option will now error by default if no
``PhaseEncodingDirection`` can be found for a BOLD series. To reduce this to
a warning, use ``--use-syn-sdc warn``. SyN-SDC will NOT be run, but the workflow
will proceed.

.. note::

``topup`` runtime scales with the number of volumes used, so fMRIPrep defaults to
using a maximum of 5 volumes from each of the BOLD series and the EPI fieldmap.
To adjust this, please use the ``--topup-max-vols`` parameter.

* FIX: Create single fmap_select_std node for use with all ANAT estimators (2692)
* FIX: Re-enable reverse-PE EPI fieldmaps (2684)
* FIX: Pass boolean use_syn_sdc to find_estimators (2685)
* FIX: Ensure AROMA inputs are uncompressed if --low-mem (2657)
* ENH: Add ``--topup-max-vols`` flag to control TOPUP runtime (2688)
* ENH: Allow ``--use-syn-sdc`` to take a "warn" option to avoid exiting when PE dir is unavailable (2680)
* RF: Add extension field to differentiate from upcoming templates (2613)
* WRAPPER: Map ``--bids-filter-file``\s into Docker container (2691)
* MNT: Silence warning from pybids; list packaging as dependency (2689)
* MNT: Add netbase to Docker image to ensure correct datalad operation (2682)
* MNT: Restore nitime to requirements, necessary for DVARS (2678)

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

=========================
Bug-fix release in the 20.2.x LTS series.

* FIX: Clarify phase encoding direction, rather than axis (2690)
* FIX: Ensure AROMA inputs are uncompressed if --low-mem (2657)
* FIX: Add ``-basescale 1`` parameter to avoid ``flirt`` scaling (2624)
* WRAPPER: Map ``--bids-filter-file``\s into Docker container (2691)
* MNT: Add netbase to Docker image to ensure correct datalad operation (2682)

=========================
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 ``CrcError``\s previously encountered.

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

=========================
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 (2573)
* CI: Add style checks (missing since Travis got throttled) (2570)