nipreps/fmriprep 21.0.0

on GitHub

Release Notes

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.

⚠️ CAUTION ⚠️

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

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.

Changes

• 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)