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Releases: nipreps/fmriprep

21.0.1

24 Jan 16:43
006c2a7
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Release Notes

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.

NOTE:

topup runtime scales with the number of volumes used, so fMRIPrep defaults to using a maximum of 5 volumes from each of the BOLD series and the EPI fieldmap. To adjust this, please use the --topup-max-vols parameter.

Changes

  • 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 (Long-Term Support)

24 Jan 16:41
c7450e7
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Release Notes

Bug-fix release in the 20.2.x LTS series.

Changes

  • 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

15 Dec 00:52
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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)

21.0.0rc2

18 Nov 21:46
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21.0.0rc2 Pre-release
Pre-release

Release Notes

A new release candidate of the upcoming 21.0.x series.
Included are some vital bug fixes, as well as improvements to susceptibility distortion correction and multi-echo derivatives.

Changes

  • 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 (LTS)

12 Nov 20:30
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Release Notes

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 CrcErrors previously encountered.

Changes

  • CI: Run full workflows on tags (#2593)
  • RF: Add extension field to differentiate from upcoming templates (#2613)

20.2.5 (Long-Term Support)

14 Oct 15:18
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DOI

Release Notes

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.

Changes

  • FIX: --slice-time-ref option parsing (#2573)
  • CI: Add style checks (missing since Travis got throttled) (#2570)
  • FIX: Resample aseg with nearest-neighbor interpolation (nipreps/smriprep#268)
  • FIX: Revert to FAST for tissue probability maps (nipreps/smriprep#264)

20.2.4 (Long-Term Support)

04 Oct 13:22
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Release Notes

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.

Changes

  • 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)

fMRIPrep 21.0.0rc1

22 Sep 14:13
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fMRIPrep 21.0.0rc1 Pre-release
Pre-release

Release Notes

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.

Changes

  • 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)

fMRIPrep 21.0.0rc0

03 Sep 14:50
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fMRIPrep 21.0.0rc0 Pre-release
Pre-release

Release Notes

The first release candidate of a new major version of fMRIPrep is here!
This release includes multiple enhancements, as well as a few bug-fixes, and features a comprehensive overhaul of susceptibility distortion correction (SDC).

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)

20.2.3

21 Jul 08:44
20.2.3
a45ea48
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Release Notes

Patch release in the 20.2.x LTS series.
Addresses minimal problems in some edge-cases, overall improves the documentation and infrastructure.
Exercises some maintenance operations addressing problems surfaced when the previous tag 20.2.2 was released.

CHANGES

  • FIX: Address the problems of a sloppy merge (#2468)
  • 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)
  • ENH: Detect 3D & too-short BOLD series, warn and skip run's workflow building (#2461)
  • 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)
  • MAINT: Containers - remove /root/.npm (#2464)
  • MAINT: Back port CircleCI configuration from dev branch (#2456)