Fmriprep

==========================
New feature release in the 22.1.x series.

This is an incremental improvement on the 22.0.x series, including features and fixes that
are backwards incompatible with the 22.0.x work tree.

Several significant issues with susceptibility distortion correction (SDC) have been fixed
in `SDCFlows 2.2.0`_, in addition to the changes listed below.
If you have been seeing issues with SDC in 21.0.x or 22.0.x, please test out this version
and submit issues.

Additionally, this version includes improvements to structural preprocessing, generating
morphometric ``.shape.gii`` files from FreeSurfer derivatives.

Finally, this release introduces a method for estimating the carbon footprint of using
fMRIPrep. Add ``--track-carbon`` to your command to try this out. Note that it does not work
in Docker containers, but should work for Singularity containers.

With thanks to Nikhil Bhagwat for contributions.


* FIX: Conform --reports-only to match post-run report generation (2900)
* FIX: Remove cortex masking during vol2surf sampling (2879)
* FIX: Do not attempt to calculate TA if SliceTiming is degenerate (2901)
* FIX: Pass CrownCompCor components to GatherConfounds (2897)
* 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)
* FIX: Filter sbrefs by BIDS filters if available (2843)
* ENH: Provide free memory estimate to unwarp_wf for better resources allocation (2910)
* ENH: Add migas telemetry in addition to sentry (2817)
* ENH: Tag memory based on data shape, annotate T2SMap (2898)
* ENH: Add of carbon tracker to estimate workflow emissions (2834)
* ENH: Output BOLD HMC transforms and reference volume (2860)
* RF: CIFTI generation (2884)
* DOC: Correct description of --longitudinal behavior (2905)
* MNT: Update fast track outputs, use latest smriprep (2894)
* MNT: Deprecate ``--topup-max-vols`` (2881)
* MNT: Add a ``--debug pdb`` to allow easier line-by-line debugging (2871)
* MNT: Generate more verbose reports (here, showing fieldmaps) if running in debug mode (2872)
* DOCKER: Build wheel and install in two-stage build (2859)
* CI: Various updates (2899)
* CI: Test on Python 3.10, bump actions versions (2895)
* CI: Fix non-fasttrack outputs for maint/21.0.x (2866)

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

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