Fmriprep

===========================
Patch release in the 22.0.x series.

This release includes relaxed tolerance in the case where fieldmap affines slightly differed,
and a fix for running FreeSurfer 7 with an outdated fsaverage folder.

* ENH: Add check to ensure latest fsaverage folder is used (2847)
* FIX: Filter sbrefs by BIDS filters if available (2843)
* FIX: Avoid crashing on empty ACompCor results (2850)

======================
New feature release in the 22.0.x series.

This release has been tested to work with Python 3.9 and FreeSurfer 7.2,
which are now bundled in the Docker image.

This release also features improvements to T2\* and carpetplot reporting.

For the next release, we are investigating issues with susceptibility
distortion correction (SDC). Please check your results carefully and report
any issues you find.

* FIX: Update wrapper python path (2783)
* FIX: Preserve ``collect_data`` behavior by using named args (2754)
* FIX: Update *fMRIPrep* version in bibliography at run time (2738)
* FIX: Plot carpetplot with CIFTI-specific colorbar (2737)
* FIX: Two minor typos in report spec (2708)
* ENH: Clip T2\* values at 100ms to keep consistent histogram axes (2781)
* ENH: Plot histogram of T2\* values in gray-matter mask (2778)
* ENH: Save T2starmap files in all requested output spaces, if calculated (2776)
* ENH: Compare T2\* map to BOLD reference (2751)
* ENH: Add edge-regressors to confounds & crown to carpetplot (2621)
* ENH: Add major/minor versions to base workflow name (2716)
* DOC: Fix JSON typo in config in FAQ (2771)
* DOC: Clarify calculation of confounding signals (2724)
* MNT: Build on Python 3.9 environment (2782)
* MNT: Seed ignore-revs file and script to tag new hashes with log entries (2748)
* MNT: Require PyBIDS 0.15+ to allow fMRIPrep to preserve zero-padding in run entity (2745)
* MNT: Upload artifacts after each step of Circle's workflow (2736)
* MNT: Normalize code style of ``workflows.confounds`` (2729)
* MNT: Ask for fmriprep-docker RUNNING line (2670)
* DOCKER: Bundle FreeSurfer 7 (2779)
* CI: Touch up CircleCI configuration (2764)
* CI: Update package builds to use python -m build (2746)

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

* FIX: Output brain mask and boldref in BOLD space if individual echos requested (2852)
* FIX: Check for empty ACompCor results before trying to rename (2851)
* CI: Fix non-fasttrack outputs for maint/21.0.x (2866)

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

This release includes a fix for `--bids-filter-file` not respecting `sbref` filtering.

* FIX: Filter sbrefs by BIDS filters if available (2843)

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