What’s new?

2.2.2 (January 04, 2023)

Patch release in the 2.2.x series.

This release resolves a bug affecting some oblique datasets.

  • RF: Generate the B-spline design matrix directly for efficiency (#324)

  • DOC: Add a notebook about susceptibility distortions (#285)

2.2.1 (December 12, 2022)

Patch release in the 2.2.x series.

This release enables dynamic estimation of memory and CPU needs for a particularly resource-intensive node.

  • ENH: Dynamically choose number of resampling threads to adapt to memory constraints (#321)

2.2.0 (December 09, 2022)

New feature release in the 2.2.x series.

This series supports fMRIPrep 22.1.x and Nibabies 22.2.x.

This release includes fixes for a number of SDC use cases.

With thanks to Basile Pinsard for adding support for fieldmaps that contribute to multiple B0FieldIdentifiers.

Attention

SDCFlows drops Python 3.7 starting with 2.2.x series.

  • FIX: Collate fieldmap coefficients into list of lists (#317)

  • FIX: Pad BSpline design matrix (#319)

  • FIX: Calculate bspline grids separately from colocation matrices (#308)

  • FIX: Support scipy 1.8 (#311)

  • FIX: Pacify deprecation warning from scipy.stats (#309)

  • FIX: Do not reorient distorted image in apply (#303)

  • FIX: Do not create a dense matrix along the way (#299)

  • FIX: Ensure replace() calls only alter the file basename (#293)

  • FIX: Update tests after merge of #287 (#288)

  • FIX: Revise debug/sloppy operations of the coeff2epi workflow (#287)

  • FIX: Revise the TOPUP workflow and related utilities (#278)

  • ENH: Default to 4mm re-zoom for b-spline approximation (#314)

  • ENH: Drop n_procs tag from BSplineApprox (#315)

  • ENH: Find B0FieldIdentifiers when one image contributes to multiple (#298)

  • ENH: Allow bids filtering during get() calls. (#292)

  • ENH: Evaluate B-Splines using scipy (#304)

  • ENH: Integrate downsampling in BSplineApprox when the input is high-res (#301)

  • ENH: Make wrangler more verbose (#284)

  • ENH: Add CLI to detect usable estimators within a BIDS dataset (#257)

  • ENH: Calculate robust average of EPI inputs to TOPUP workflow (#280)

  • MAINT: Housekeeping and more verbose debugging outputs (#302)

  • MAINT: Simplify build tests on GH Actions to latest standards (#282)

  • MAINT: Keep CircleCI settings up to date (#281)

  • MAINT: Unavilable data from OSF remote (datalad) for CircleCI tests. (#277)

  • MAINT: Remove unused argument from topup related interface (#276)

  • CI: Update concurrency, permissions and actions (#313)

  • CI: Roll unittests runner back to Ubuntu 20.04 (#310)

  • CI: Ensure builds are triggered weekly (#270)

2.1.1 (August 29, 2022)

Patch release in the 2.1.x series. This release incorporates the fix in 2.0.13 in the 2.1.x series.

  • FIX: Relax tolerance for different affines when concatenating blips (#265)

2.1.0 (May 26, 2022)

A new minor release to support the newest niworkflows minor series.

  • ENH: Add optional session distinction to wrangler (#261)

  • FIX: Align centers of mass, rather than origins (#253)

  • MAINT: Loosen installation restrictions (#269)

2.0.13 (April 08, 2022)

Patch release in the 2.0.x series. This release resolves an issue in fMRIPrep 21.0.x.

  • FIX: Relax tolerance for different affines when concatenating blips (#265)

2.0.12 (February 08, 2022)

Patch release in the 2.0.x series. This allows compatibility with the next minor release of niworkflows.

  • MAINT: Allow compatibility with new niworkflows minor (#262)

  • DOC: Update scipy intersphinx url (#263)

2.0.11 (January 22, 2022)

Patch release in the 2.0.x series.

  • FIX: Create one fieldmap estimator per EPI-IntendedFor pair (#258)

  • DOCKER: Build with FSL 6 (#254)

2.0.10 (December 13, 2021)

Patch release in the 2.0.x series.

  • FIX: Update boilerplate ordering directives (#229)

  • FIX: ishandling of topup coefficients with higher resolution EPIs (#251)

2.0.9 (November 16, 2021)

A patch release improving documentation and implementing B0Field* BIDS metadata.

  • DOC: Bring implementation details to the foreground of documentation (#248)

  • FIX: Implement B0FieldIdentifier / B0FieldSource (#247)

2.0.8 (October 15, 2021)

A patch release with a deep revision of the new implementation of the fieldmap-less “SDC-SyN” toward integration with fMRIPrep.

  • FIX: SDC-SyN (“fieldmap-less”) overhaul (#239)

  • DOC: Self-hosted & multiversion documentation overhaul (#243)

  • MAINT: Standardization of containers across NiPreps (#240)

2.0.7 (September 30, 2021)

A patch release with important bugfixes discovered during the integration with fMRIPrep.

  • FIX: Generation of RAS displacements fields from VSMs (#237)

  • FIX: Use subject root to resolve IntendedFor paths (#228)

  • ENH: Improve support of 4D in sdcflows.interfaces.bspline.ApplyCoeffsField (#234)

  • MAINT: Update node and gh-pages, push docs without history (#230)

2.0.6 (September 1, 2021)

A patch release to address a problem with TOPUP and an odd number of slices.

  • ENH: Add slice padding to TOPUP (#217)

2.0.5 (August 24, 2021)

A bugfix release, adds the fieldwarp as an output to the unwarping workflow.

  • FIX: The calculated displacements field not exposed by unwarp workflow (#224)

  • MAINT: Use keys.openpgp.org over sks-keyservers (#223)

2.0.4 (May 18, 2021)

A hotfix release including some enhancements that should have been released within the previous 2.0.3 release.

  • ENH: Fine-tune the registration parameters in coeff2epi workflow (#215)

  • ENH: Finalize upstreaming to NiWorkflows of IntensityClip (#216)

  • ENH: Use new RobustAverage interface to merge corrected blips (#214)

  • DOC: Insert copyright notice in header comments as per Apache-2.0 (#212)

2.0.3 (May 14, 2021)

A patch release including some improvements to the PEPOLAR/TOPUP implementation, along with corresponding updates to the CI tests.

  • ENH: Uniformize the grid&affine across EPI “blips” before TOPUP (#197)

  • MAINT: Fix PEPOLAR workflow test with HCP data (#210)

  • MAINT: Update tests after changes in ds001771’s structure (#209)

2.0.2 (May 11, 2021)

A patch release including hot-fixes and some relevant improvements inteded for the reliability of the new API. The most relevant advance is the new \(B_0\) fieldmap unwarping object which is compatible with NiTranforms and evades the problem of fiddling with the target image’s x-forms.

  • FIX: Make sure the VSM is not modified when accessing it (#207)

  • FIX: Normalize phase-encoding polarity of coefficients after TOPUP (#202)

  • FIX: Revise generation of the displacements field from coefficients (#199)

  • FIX: Inconsistency left after renaming inputs to SDC-SyN (removing “BOLD”) (#182)

  • FIX: Correctly interpolate the BIDS root when datasets have sessions (#180)

  • ENH: \(B_0\) fieldmap unwarping object (#204)

  • ENH: Add estimation method description to outputs (#191)

  • ENH: Ensure a function node is covered with unit tests (#188)

  • ENH: Add a preprocessing pipeline for SDC-SyN (#184)

  • ENH: [rodents] Add input to override default B-Spline distances in INU correction with N4 (#178)

  • ENH: Adopt new brain extraction algorithm in magnitude preparation workflow (#176)

  • DOC: Fix typos as per codespell (#205)

  • MAINT: Double-check conversion from TOPUP to standardized fieldmaps (#200)

  • MAINT: Divide ambiguous debug parameter into smaller, more focused parameters (#190)

  • MAINT: Adapt to GitHub actions’ upgrade to Ubuntu 20.04 (#185)

2.0.1 (March 05, 2021)

A patch release including some bugfixes and minimal improvements over the previous major release.

  • FIX: Inconsistency left after renaming inputs to SDC-SyN (removing “BOLD”) (#182)

  • FIX: Correctly interpolate the BIDS root when datasets have sessions (#180)

  • ENH: Add a preprocessing pipeline for SDC-SyN (#184)

  • ENH: [rodents] Add input to override default B-Spline distances in INU correction with N4 (#178)

  • ENH: Adopt new brain extraction algorithm in magnitude preparation workflow (#176)

  • MAINT: Adapt to GitHub actions’ upgrade to Ubuntu 20.04 (#185)

2.0.0 (January 25, 2021)

The SDCFlows 2.0.x series are released after a comprehensive overhaul of the software’s API. This overhaul has the vision of converting SDCFlows into some sort of subordinate pipeline to other d/fMRIPrep, inline with sMRIPrep’s approach. The idea is to consider fieldmaps a first-citizen input, for which derivatives are generated at the output (on the same vein of, and effectively implementing #26). A bids’s-eye view of this new release follows:

  • Two new base objects (FieldmapFile and FieldmapEstimation) for the validation and representation of fieldmap estimation strategies. Validation of metadata and checking the sufficiency of imaging files and necessary parameters is now done with these two objects. FieldmapEstimation also generates the appropriate estimation workflow for the input data.

  • Moved estimation workflows under the sdcflows.workflows.fit module.

  • New outputs submodule sdcflows.workflows.outputs that writes out reportlets and derivatives, following suit with higher-level NiPreps (s/f/dMRIPrep). The two workflows are exercised in the CircleCI tests, and the artifacts are generated this way. Derivatives are populated with relevant pieces of metadata (for instance, they forward the IntendedFor fields).

  • A new init_fmap_preproc_wf(), leveraging FieldmapEstimation objects.

  • Separated out a new utilities module sdcflows.utils for the manipulation of phase information and EPI data.

  • New sdcflows.workflows.apply.registration module, which aligns the reference map of the fieldmap of choice (e.g., a magnitude image) to the reference EPI (e.g., an SBRef, a b=0 DWI, or a fMRIPrep’s BOLDRef) with ANTs. The workflow resamples the fieldmap reference into the reference EPI’s space for reporting/visualization objectives.

  • New sdcflows.interfaces.bspline set of utilities for the filtering and extrapolation of fieldmaps with B-Splines. Accordingly, all workflows have been updated to correctly handle (and better use) B-Spline coefficients.

  • A new PEPOLAR implementation based on TOPUP (see sdcflows.workflows.fit.pepolar.init_topup_wf()).

  • Pushed the code coverage with tests, along with a deep code cleanup.

Attention

SDCFlows drops Python 3.6 starting with 1.4.x series.

Some of the most prominent pull-requests conducive to this release are:

  • FIX: Fast & accurate brain extraction of magnitude images without FSL BET (#174)

  • FIX: svgutils 0.3.2 breaks our reportlets (#175)

  • FIX: Misconfigured test of unwarping workflow (#170)

  • FIX: Cleanup annoying isolated dots in reportlets + new tests (#168)

  • FIX: Make images “plumb” before running ANTs-SyN (and roll-back afterwards) (#165)

  • FIX: Convert SEI fieldmaps given in rad/s into Hz (#127)

  • FIX: Limit 3dQwarp to maximum 4 CPUs for stability reasons (#128)

  • ENH: Adopt new brain extraction algorithm in magnitude preparation workflow (#176)

  • ENH: Add “fieldmap-less” estimations to default heuristics (#166)

  • ENH: Add one test for the SDC-SyN workflow (#164)

  • ENH: Generate a simple mask after correction (#161)

  • ENH: Increase unit-tests coverage of sdcflows.fieldmaps (#159)

  • ENH: Optimize tensor-product B-Spline kernel evaluation (#157)

  • ENH: Add a memory check to dynamically limit interpolation blocksize (#156)

  • ENH: Massage TOPUP’s fieldcoeff files to be compatible with ours (#154)

  • ENH: Add a simplistic EPI masking algorithm (#152)

  • ENH: Utility that returns the B0FieldSource of a given potential EPI target (#151)

  • ENH: Write fmapid- entity in Derivatives (#150)

  • ENH: Multiplex fieldmap estimation outputs into a single outputnode (#149)

  • ENH: Putting the new API together on a base workflow (#143)

  • ENH: Autogenerate B0FieldIdentifiers from IntendedFor (#142)

  • ENH: Finalizing the API overhaul (#132)

  • ENH: Keep a registry of already-used identifiers (and auto-generate new) (#130)

  • ENH: New objects for better representation of fieldmap estimation (#114)

  • ENH: Show FieldmapReportlet oriented aligned with cardinal axes (#120)

  • ENH: New estimation API (featuring a TOPUP implementation!) (#115)

  • DOC: Minor improvements to the literate workflows descriptions. (#162)

  • DOC: Fix typo in docstring (#155)

  • DOC: Enable NiPype’s sphinx-extension to better render Interfaces (#131)

  • MAINT: Docker - Update base Ubuntu image & ANTs, makefile (#173)

  • MAINT: Retouch several tests and improve ANTs version handling of SyN workflow (#172)

  • MAINT: Drop Python 3.6 (#160)

  • MAINT: Enable Git-archive protocol with setuptools-scm-archive (#153)

  • MAINT: Migrate TravisCI -> GH Actions (completion) (#138)

  • MAINT: Migrate TravisCI -> GH Actions (#137)

  • MAINT: Minimal unit test and refactor of pepolar workflow node (#133)

  • MAINT: Collect code coverage from tests on Circle (#122)

  • MAINT: Test minimum dependencies with TravisCI (#96)

  • MAINT: Add FLIRT config files to prepare for TOPUP integration (#116)

A complete list of issues addressed by the release is found in the GitHub repo.

Author list for papers based on SDCFlows 2.0.x series

As described in the Contributor Guidelines, anyone listed as developer or contributor may write and submit manuscripts about SDCFlows. To do so, please move the author(s) name(s) to the front of the following list:

Markiewicz, Christopher J. 1; Goncalves, Mathias 1; MacNicol, Eilidh 2; Adebimpe, Azeez 3; Blair, Ross W. 1; Cieslak, Matthew 3; Naveau, Mikaël 4; Sitek, Kevin R. 5; Sneve, Markus H. 6; Gorgolewski, Krzysztof J. 1; Satterthwaite, Theodore D. 3; Poldrack, Russell A. 1; Esteban, Oscar 7.

Affiliations:

  1. Department of Psychology, Stanford University

  2. Department of Neuroimaging, King’s College London

  3. Perelman School of Medicine, University of Pennsylvania, PA, USA

  4. Cyceron, UMS 3408 (CNRS - UCBN), France

  5. Speech & Hearing Bioscience & Technology Program, Harvard University

  6. Center for Lifespan Changes in Brain and Cognition, University of Oslo

  7. Dept. of Radiology, Lausanne University Hospital, University of Lausanne

1.3.x series

1.3.3 (September 4, 2020)

Bug-fix release in 1.3.x series.

Allows niworkflows 1.2.x or 1.3.x, as no API-breaking changes in 1.3.0 affect SDCflows.

1.3.2 (August 14, 2020)

Bug-fix release in 1.3.x series.

  • FIX: Replace NaNs in fieldmap atlas with zeros (#104)

  • ENH: Return out_warp == “identity” if no SDC is applied (#108)

1.3.1 (May 22, 2020)

Bug-fix release adapting to use newly refacored DerivativesDataSink

  • ENH: Use new DerivativesDataSink from NiWorkflows 1.2.0 (#102)

1.3.0 (May 4, 2020)

Minor release enforcing BIDS-Derivatives labels on dseg file.

  • FIX: WM mask selection from dseg before generating report (#100)

Pre-1.3.x releases

1.2.2 (April 16, 2020)

Bug-fix release to fix phase-difference masking bug in the 1.2.x series.

  • FIX: Do not reorient magnitude images (#98)

1.2.1 (April 01, 2020)

A patch release to make SDCFlows more amicable to downstream software.

  • MAINT: Migrate from versioneer to setuptools_scm (#97)

  • MAINT: Flexibilize dependencies – nipype, niworkflows, pybids (#95)

1.2.0 (February 15, 2020)

A minor version release that changes phasediff caclulations to improve robustness. This release is preparation for fMRIPrep 20.0.0.

  • FIX: Scale all phase maps to [0, 2pi] range (#88)

  • MNT: Fix package tests (#90)

  • MNT: Fix circle deployment (#91)

1.1.0 (February 3, 2020)

This is a nominal release that enables downstream tools to depend on both SDCFlows and niworkflows 1.1.x.

Bug fixes needed for the 1.5.x series of fMRIPrep will be accepted into the 1.0.x series of SDCFlows.

1.0.6 (April 15, 2020)

Bug-fix release.

  • FIX: Do not reorient magnitude images (#98)

1.0.5 (February 14, 2020)

Bug-fix release.

  • FIX: Center phase maps around central mode, avoiding FoV-related outliers (#89)

1.0.4 (January 27, 2020)

Bug-fix release.

  • FIX: Connect SyN outputs whenever SyN is run (#82)

  • MNT: Skim Docker image, optimize CircleCI workflow, and reuse cached results (#80)

1.0.3 (December 18, 2019)

A hotfix release preventing downstream dependency collisions on fMRIPrep.

1.0.2 (December 18, 2019)

A hotfix release.

  • FIX: NiWorkflows’ IntraModalMerge choked with images of shape (x, y, z, 1) (#79, 2e6faa0, 717a69e, and 361cd67)

1.0.1 (December 04, 2019)

A bugfix release.

  • FIX: Flexibly and cheaply select initial PEPOLAR volumes (#75)

  • ENH: Phase1/2 - subtract phases before unwrapping (#70)

1.0.0 (November 25, 2019)

A first stable release after detaching these workflows off from fMRIPrep.

With thanks to Matthew Cieslak and Azeez Adebimpe.

  • FIX: Hard-wire MNI152NLin2009cAsym as standard space for SDC-SyN (#63)

  • ENH: Base implementation for phase1/2 fieldmaps (#60)

  • ENH: Update spatialimage.get_data() -> spatialimage.get_fdata() (#58)

  • ENH: Refactor fieldmap-unwarping flows, more homogeneous interface (#56)

  • ENH: Transparency on fieldmap plots! (#57)

  • ENH: Stop using siemens2rads from old nipype workflows (#50)

  • ENH: Large refactor of the orchestration workflow (#55)

  • ENH: Refactor the distortion estimation workflow (#53)

  • ENH: Deduplicating magnitude handling and fieldmap postprocessing workflows (#52)

  • ENH: Do not use legacy demean function from old nipype workflows (#51)

  • ENH: Revise and add tests for the PEPOLAR correction (#29)

  • ENH: Improved fieldmap reportlets (#28)

  • ENH: Set-up testing framework (#27)

  • DOC: Update documentation (#61)

  • DOC: Fix typo and link to BIDS Specification (#49)

  • DOC: Build API documentation (#43)

  • CI: Add check to avoid deployment of documentation from forks (#48)

  • CI: Fix CircleCI builds by adding a [refresh workdir] commit message tag (#47)

  • CI: Optimize CircleCI using a local docker registry instead docker save/load (#45)

  • MAINT: Housekeeping - flake8 errors, settings, etc. (#44)

  • MAINT: Rename boldrefs to distortedrefs (#41)

  • MAINT: Use niflow-nipype1-workflows for old nipype.workflows imports (#39)

0.1.4 (November 22, 2019)

A maintenance release to pin niworkflows to version 1.0.0rc1.

0.1.3 (October 15, 2019)

Adapts SDCflows to the separation of workflows from Nipype 1.

  • MAINT: pin niflow-nipype1-workflows, nipype and update corresponding imports.

0.1.2 (October 10, 2019)

BAD RELEASE – DO NOT USE

0.1.1 (July 23, 2019)

Minor fixup of the deploy infrastructure from CircleCI

  • MAINT: Add manifest including versioneer (#25) @effigies

0.1.0 (July 22, 2019)

First version working with fMRIPrep v1.4.1.