21.0.4 (September 29, 2022)

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)

22.0.2 (September 27, 2022)

A patch release in the 22.0.x series.

This release increases the minimum Nipype version to include better error messages on failures.
Additionally, this includes a fix to allow SyN distortion correction in combination with the
`--ignore fieldmaps` option.

  * MAINT: Add `pre-commit`, dev installation for consistent styling (#2857)
  * CI: Upgrade docker orb (#2858)

22.0.1 (September 13, 2022)
===========================
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and a fix for running FreeSurfer 7 with an outdated fsaverage folder.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)

21.0.3 (September 6, 2022)

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)

22.0.0 (July 28, 2022)

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)

22.0.0rc4 (21 July 2022)

Hopefully the last...

22.0.0rc3 (July 1, 2022)
=======================

This release candidate fixes an error that was encountered
filtering sessions with the `--bids-filter-file`.

22.0.0 (To be determined)
      New feature release in the 22.0.x series.

This release candidate includes missing FreeSurfer binaries that would result
in `recon-all` sometimes failing.

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.

  * FIX: Re-add fsr-checkxopts to Docker image
  * 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)

22.0.0 (To be determined)

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.

  * FIX: Re-add fsr-checkxopts to Docker image
  * 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)

22.0.0rc0

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.

  * 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)

21.0.2 (April 21, 2022)
=======================
Bug-fix releaase 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/niworkflows#706)
  * 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/niworkflows#719)
  * FIX: Improve reliability of BOLD masking workflow (nipreps/niworkflows#712)
  * FIX: Relax tolerance for different affines when concatenating blips (nipreps/sdcflows#265)

21.0.1 (January 24, 2022)

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.

* 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)

20.2.7 (January 24, 2022)

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)

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)

21.0.0rc2 (November 18, 2021)
-----------------------------
* DOC: ME | Add missing output to documentation, improve boilerplate (#2608)
* ENH: Tedana-friendly ME derivatives (#2575)
* ENH: Better integration of *SDCFlows*' unwarping (#2576)
* ENH: Refactor workflow to adopt *SDCFlows*' new correction workflow (#2547)
* 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)
* 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)

20.2.6 (October 27, 2021)
=========================
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)

20.2.5 (October 12, 2021)

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)

20.2.4 (October 04, 2021)

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.

  * 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)

21.0.0rc1 (September 21, 2021)
=============================
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.

* 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)

21.0.0rc0 (September 2, 2021)
=============================
The first release candidate for a new major version of fMRIPrep!

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)