24.0

[effigies]

24.0.0

Release notes

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!

Changes

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

New Contributors

• @htwangtw made their first contribution in DOC: clarify --dvars-spike-threshold uses standardized DVARS #3205

Full Changelog: 23.2.3...24.0.0

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This discussion was created from the release 24.0.0.

[effigies]

24.0.1

Release notes

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.

Changes

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

Full Changelog: 24.0.0...24.0.1