Fmriprep

===========================
New feature release in the 24.1.x series.

Handling of gradient echo fieldmaps is improved.

* FIX: Select volumetric dseg.tsv from recent TemplateFlow releases (3257)
* RF: Adapt to less T1w-centric smriprep (3333)
* RF: Use acres over vendored data loader (3323)
* DOC: Add benchmark page (3312)
* MAINT: Move to tox to simplify test/CI setup (3326)
* CI: Fix expected outputs for fieldmaps (3321)

======================
Bug fix release in the 24.0.x series.

This release resolves a bug with multi-volume single-band references.
If multiple volumes are found, they are processed in the same way as
the BOLD series is processed to produce a motion-correction reference.

* FIX: Validate and summarize multi-volume sbrefs (3320)
* DOC: Address errors/warnings in RTD builds (3325)
* DOC: Read html_baseurl from RTD environment, if available (3324)

======================
New feature release in the 24.0.x series.

This release is an incremental improvement on 23.2.x, with some
fixes for bugs discovered in the updated workflow.

New features include separation of HTML reports by session for subjects
with many BOLD runs, a new ``--fs-no-resume`` option to improve interoperability
with less typical FreeSurfer directories, such as those generated by longitudinal
FreeSurfer or FastSurfer, and adoption of DatasetLinks and BIDS-URIs, to follow
the recommendations of recent versions of BIDS.

With thanks to Dimitri Papadopoulos, Basile Pinsard, Celine Provins, Taylor Salo
and Wang Hao-Ting for their contributions!

* FIX: Add "double" type to allowed DisplacementFieldTransform (3287)
* FIX: Require recent templateflow, select correct aparc dseg.tsv (3256)
* FIX: Ensure proper templates are retrieved with sloppy (3251)
* FIX: Delete summary from functional report when separated by sessions (3223)
* FIX: Support lists in bids filter file containing ``null`` or ``*`` (3215)
* FIX: Re-enable anat fasttrack for dataset without t1w (3202)
* ENH: Use BIDSURI in init_ds_boldmask_wf (3297)
* ENH: Add templateflow to DatasetLinks (3267)
* ENH: Track proximal sources of functional GIFTIs (3263)
* ENH: Support named derivative paths (3264)
* ENH: Track Sources for standard-space outputs (3262)
* ENH: Add --fs-no-resume option to reuse existing FreeSurfer outputs without resuming (3142)
* ENH: Use BIDS URIs to track Sources in sidecars (3255)
* ENH: Ignore unselected subjects in BIDSLayoutIndexer (3236)
* ENH: Add metadata for motion parameters (3245)
* ENH: Separate anatomical and functional reports per session for densely sampled dataset (3191)
* ENH: Leverage T2w if available for BOLD -> anat coregistration (3208)
* RF: Fix ITK warp conversion to nitransforms format (3300)
* RF: Load report assembler from nireports (3177)
* DOC: Clarify ``--dvars-spike-threshold`` uses standardized DVARS (3205)
* TST: Update test to reflect new report generation behavior (3210)
* STY: Manual conversions to f-strings (3241)
* STY: Apply ruff/pyupgrade rule UP031 (3280)
* STY: Lint and style check full repository (3221)
* STY: Adopt ruff for linting and formatting (3206)
* MNT: Pin libitk 5.3 and note dependencies (3298)
* MNT: Upgrade ruff pre-commit, add fixing checks (3283)
* MNT: Complete transition from flake8/black to ruff (3279)
* MNT: Apply Repo-Review suggestions (3194)
* MNT: Verbatim copy of Apache license 2.0 (3259)
* MNT: Bump cryptography from 41.0.7 to 42.0.4 (3234)
* MNT: Drop copyright year, unused dunder fields (3247)
* MNT: Update environment pins (3226)
* MNT: Bump codecov/codecov-action from 3 to 4 (3219)
* DOCKER: Restore mincinfo binary (3249)
* CI: Move to new circle machine tags (3248)
* CI: Avoid ruff warning (3244)
* CI: Pass ruff tests (3243)

=====================
Bug fix release in the 23.2.x series.

Writes brain masks in ``space-boldref`` with ``--level minimal``,
bringing behavior in line with documentation.

* FIX: Write out boldref-space brain mask with minimal level (3292)

=====================
Bug fix release in the 23.2.x series.

Fixes an issue with broken connections, which only affects ``--level resampling``.

* FIX: Add datasink fill-in step to resampling level (3254)

=======================
Bug fix release in the 23.2.x series.

Masks, BOLD references and T2\* maps resampled into template spaces had
their order of transforms inverted. BOLD files were unaffected.

This release also preserves the TR in the NIfTI header of BOLD series.

* FIX: Preserve pixdim4+ of resampled images (3239)
* FIX: Flip order of transforms in ``init_ds_volumes_wf`` (3238)
* DOCKER: restore mincinfo binary (3249)
* CI: Move to new CircleCI machine tags (3247)