sdcflows - 2.13.2

Release Notes

Patch release in the 2.13.x series.

This includes a fix for cases where a scan contributes to multiple B0FieldIdentifiers.

Changelog

• FIX: Fixes conditions of overlapping B0FieldIdentifier, resulting in no estimators (https://github.com/nipreps/sdcflows/pull/497)

- Python
Published by mgxd 11 months ago

sdcflows - 2.13.1

Release Notes

Patch release in the 2.13.x series.

This includes a fix to init_fmap_preproc_wf node naming.

Changes

• FIX: Use the sanitized id when naming through nipype (https://github.com/nipreps/sdcflows/pull/495)

- Python
Published by mgxd about 1 year ago

sdcflows - 2.13.0

Release Notes

Feature release in the 2.13.x series.

This release addresses some longstanding issues with the SyN-SDC workflow, improving the registration quality in adult humans by utilizing a spatial prior, as well as allowing Laplacians to be up- or down-weighted in the cost function, making it more usable across species.

Additionally, this release allows for the use of EstimatedTotalReadoutTime or EstimatedEchoSpacing, or a manually provided fallback TotalReadoutTime value, permitting the use of SDCFlows on datasets that do not have reliable timing information without introducing incorrect metadata into the datasets.

Changes

• fix(syn): Re-enable priors respecting sd_priors argument (https://github.com/nipreps/sdcflows/pull/488)
• feat: Add workflow arguments for metadata estimates and fallback TRT (https://github.com/nipreps/sdcflows/pull/479)
• feat(syn): Update totalFieldVarianceInVoxel space based on voxel resolution (https://github.com/nipreps/sdcflows/pull/487)
• feat(syn): Allow changing laplacians weights in SyN registration metric (https://github.com/nipreps/sdcflows/pull/484)
• test(syn): Add a test to exercise SyN workflow creation and check parameters (https://github.com/nipreps/sdcflows/pull/486)

- Python
Published by mgxd about 1 year ago

sdcflows - 2.12.0

Release Notes

This release migrates from the deprecated niworkflows.reporting module to the nireports package.

Changes

• FIX: AttributeError for _ApplyCoeffsFieldInputSpec (#481)
• ENH: Allow running SyN SDC without using prior (#480)
• ENH: Allow estimated and fallback TotalReadoutTime (#477)
• RF: Transition from niworkflows reporting interfaces (#473)
• DOC: Fix broken link skip ci
• MNT: Add defaults to conda channels in build-test-publish GHA (#474)
• MNT: Update niworkflows version to 1.11.0 (#478)

- Python
Published by mgxd about 1 year ago

sdcflows - 2.11.0

Release notes

Feature release in the 2.11.x series.

This release supports numpy 2 and Python 3.13.

Changes

• FIX: Normalize BIDS-URIs to subject-relative (#458)
• FIX: Only fit high-frequency spline for SyN-SDC (#457)
• ENH: Allow Jacobian correction to be toggled on/off (#462)
• ENH: Dilate fmap and bold masks during coregistration (#463)
• TEST: Clear registry consistently to avoid order dependency (#464)
• DOC: Plot correct workflow in initsynpreprocessing_wf docstring (#460)
• CI: Drop CircleCI, using GHA only (#459)

New Contributors

• @psadil made their first contribution in https://github.com/nipreps/sdcflows/pull/463

Full Changelog: https://github.com/nipreps/sdcflows/compare/2.10.0...2.11.0

- Python
Published by effigies over 1 year ago

sdcflows - 2.10.0

Release Notes

Feature release in the 2.10.x series.

The main change is a bugfix when fitting multi-level B-Splines to some noisy fieldmaps. While theoretically nice, the multi-level fitting does not really bring anything immediately as we are not generally inverting the distortion. In this release, the default fitting has been changed to single-level B-Splines, with a spacing similar to TOPUP's defaults.

With thanks to Sunjae Shim (@sjshim) for sharing Spiral-echo fieldmaps that were failing prior the patch in #453.

What's Changed

• FIX: Building Docker image on ARM64 devices by @mathdugre in https://github.com/nipreps/sdcflows/pull/449
• DOC: ValueError in notebook output by @mathdugre in https://github.com/nipreps/sdcflows/pull/450
• ENH: Improve plots in Jupyter notebook by @oesteban in https://github.com/nipreps/sdcflows/pull/452
• FIX: Revision of the B-Spline fitting code by @oesteban in https://github.com/nipreps/sdcflows/pull/453

New Contributors

• @mathdugre made their first contribution in https://github.com/nipreps/sdcflows/pull/449

Full Changelog: https://github.com/nipreps/sdcflows/compare/2.9.0...2.10.0

- Python
Published by oesteban almost 2 years ago

sdcflows - 2.9.0

Release notes

Feature release in the 2.9.x series.

The main change is that B0FieldIdentifiers with special characters are now sanitized and exposed through a FieldmapEstimator.sanitized_id attribute.

Workflow names and input/output connections will use sanitized_id, to ensure compatibility with filenames and workflow graph generation. Internal lookup tables will continue to use the the unsanitized bids_id.

Changes

• FIX: Update suffix only when finding related fieldmap files (https://github.com/nipreps/sdcflows/pull/436)
• RF: Add sanitized_id field to FieldmapEstimation (https://github.com/nipreps/sdcflows/pull/444)
• DOC: Un-mock the already-imported numpy (https://github.com/nipreps/sdcflows/pull/440)
• CI: Bump actions/cache from 3 to 4 (https://github.com/nipreps/sdcflows/pull/429)

New Contributors

• @marcelzwiers made their first contribution in https://github.com/nipreps/sdcflows/pull/436

Full Changelog: https://github.com/nipreps/sdcflows/compare/2.8.1...2.9.0

- Python
Published by effigies about 2 years ago

sdcflows - 2.8.1

Release notes

Bug-fix release in the 2.8.x series.

Fixes doc builds and CLI support for fieldmapless workflows. Introduces support for BIDS-URIs.

Changes

• FIX: Enable fieldmapless by default in CLI (#426)
• FIX: Pandoc requires Texlive to render LaTeX in notebook (#427)
• FIX: New test test_wrangler_URIs had the wrong oracle (#425)
• ENH: Resolve BIDS-URIs (#349)
• TEST: Use less confusing function name for testing CLI with --dry-run (#424)
• MNT: Bump actions/download-artifact from 3 to 4 (#418)
• MNT: Bump actions/upload-artifact from 3 to 4 (#417)
• CI: Move PR doc build into main doc build, add texlive to build dependencies (#428)

Full Changelog: https://github.com/nipreps/sdcflows/compare/2.8.0...2.8.1

- Python
Published by effigies over 2 years ago

sdcflows - 2.8.0

Release notes

New feature release in the 2.8.x series.

This release fixes a bug in converting SyN-SDC displacements to fieldmaps, resulting in exaggerated corrections. As this makes changes to the structure of a workflow and the expected inputs of a workflow node, this release is considered a minor release.

Changes

• FIX: Derive field from SyN displacements using EPI affine (#421)
• FIX: Change os.basename to os.path.basename (#419)
• DOC: Add @smeisler to contributors (#420)

New Contributors

• @smeisler made their first contribution in https://github.com/nipreps/sdcflows/pull/419

Full Changelog: https://github.com/nipreps/sdcflows/compare/2.7.0...2.8.0

- Python
Published by effigies over 2 years ago

sdcflows - 2.7.0

Release notes

New feature release in the 2.7.x series.

This release includes an updated CLI, which allows sdcflows to be run as a BIDS App. To achieve the previous behavior of sdcflows-find-estimators, use the -n flag.

Addtional bug fixes and enhancements are included.

Changes

• FIX: Drop header before resampling image to avoid unsafe cast (#415)
• FIX: Wrangler now ignores part-phase EPI files (#407)
• ENH: Standalone CLI now estimates fieldmaps (#408)
• ENH: Add support for ASL data (#411)
• ENH: Enable rendering of the Jupyter notebooks (#409)
• MNT: Migrate to PEP517/518 packaging (#410)
• CI: bump actions/setup-python from 4 to 5 (#412)
• CI: bump conda-incubator/setup-miniconda from 2 to 3 (#406)

New Contributors

• @tsalo made their first contribution in https://github.com/nipreps/sdcflows/pull/411

Full Changelog: https://github.com/nipreps/sdcflows/compare/2.6.0...2.7.0

- Python
Published by effigies over 2 years ago

sdcflows - 2.6.0

Release Notes

New feature release in the 2.6.0 series.

This release resolves a number of issues with fieldmaps inducing distortions during correction. Phase difference and direct fieldmaps are now masked correctly, preventing the overestimation of distortions outside the brain. Additionally, we now implement Jacobian weighting during unwarping, which corrects for compression and expansion effects on signal intensity.

Changes

• FIX: Mask fieldmap before fitting spline field (https://github.com/nipreps/sdcflows/pull/396)
• FIX: Interpolate to floating point values (https://github.com/nipreps/sdcflows/pull/394)
• FIX: Refactoring the B0FieldTransform implementation (https://github.com/nipreps/sdcflows/pull/346)
• FIX: Nipype workflows like to be passed absolute paths (phasediff fieldmap) (https://github.com/nipreps/sdcflows/pull/374)
• ENH: Implement Jacobian weighting during unwarp (https://github.com/nipreps/sdcflows/pull/391)
• ENH: Output target2fmapxfm from coeff2epiwf (https://github.com/nipreps/sdcflows/pull/381)
• ENH: Add data loader to sdcflows.data, drop pkg_resources (https://github.com/nipreps/sdcflows/pull/379)
• RF: Use scipy.interpolate.BSpline to construct spline basis (https://github.com/nipreps/sdcflows/pull/393)
• DOC: Use latest sphinx to fix bad sphinx/furo interaction (https://github.com/nipreps/sdcflows/pull/390)
• DOC: Fix missing dependency when merging new data loader (https://github.com/nipreps/sdcflows/pull/380)
• MNT: Update emprical values in test to allow transition to new scipy's BSpline (https://github.com/nipreps/sdcflows/pull/387)
• MNT: Add pre-commit config (https://github.com/nipreps/sdcflows/pull/375)
• MNT: Add a seed to random generator of coefficients (https://github.com/nipreps/sdcflows/pull/368)

- Python
Published by mgxd over 2 years ago

sdcflows - 2.5.2

Release Notes

Bug-fix release in the 2.5.x series.

This release includes a fix for phasediff/direct fieldmaps that were previously producing distortions outside the brain due to an incorrect masking of the fieldmap.

Changes

• FIX: Mask fieldmap before fitting spline field backport https://github.com/nipreps/sdcflows/pull/396
• DOC: Fix doc build for 2.5.x branch (https://github.com/nipreps/sdcflows/pull/399)
• MAINT: Make call to scipy.stats.mode compatible with scipy 1.11.0 (https://github.com/nipreps/sdcflows/pull/371)

- Python
Published by mgxd over 2 years ago

sdcflows - 2.5.1

Release Notes

Bug-fix release in the 2.5.x series.

Changes

• FIX: Use lsqr solver for spline fit, rerun on extreme values (https://github.com/nipreps/sdcflows/pull/366)
• FIX: Ensure metadata is not present in entity query (https://github.com/nipreps/sdcflows/pull/367)
• RF/FIX: Prioritize sbref and shortest echo for SyN-SDC (https://github.com/nipreps/sdcflows/pull/364)

- Python
Published by mgxd over 2 years ago

sdcflows - 2.5.0

Release notes

New feature release in the 2.5.x series.

This release includes a number of changes to default behaviors. SyN-SDC will be performed per-BOLD/DWI image, unless specified otherwise with B0FieldIdentifiers, and may now be specified with T2w images as anatomical references as well. Additionally, PEPolar fieldmaps will only be grouped if they share IntendedFor metadata.

Finally, as a small UX improvement, if magnitude1/magnitude2 images have differing affines but are in register, we will now copy the header rather than requiring the user to update the header themselves.

Changes

• FIX: Ensure IntendedFor metadata is a subject-relative path (#360)
• ENH: Split SyN fieldmap estimates per-EPI (#312)
• ENH: Allow non-T1w anatomical estimators (#358)
• ENH: Function to calculate reference grids aligned with the coefficients (#355)
• ENH: Check registration of magnitude1/magnitude2 images and update headers (#356)
• RF: Split PEPolar fieldmaps by intent, if available (#342)
• CI: Use supported codecov uploaders (#348)

Full Changelog: https://github.com/nipreps/sdcflows/compare/2.4.3...2.5.0

- Python
Published by effigies about 3 years ago

sdcflows - 2.4.3

Release Notes

Bug-fix release in the 2.4.x series.

This fix resolves an inconsistency of treatment of phase-difference and scanner-calculated fieldmaps, relative to PEPolar and SyN. Fieldmaps in orientations other than RAS were impacted.

Changes

• FIX: Reorient fieldmaps to RAS before estimating B-splines (#354)

- Python
Published by effigies about 3 years ago

sdcflows - 2.4.2

Release Notes

Bug-fix release in the 2.4.x series.

Same fixes as 2.4.1, but this time for phase-difference and direct fieldmaps we missed last time.

Changes

• FIX: Capture and report partial fieldmaps (#351)

- Python
Published by effigies about 3 years ago

sdcflows - 2.4.1

Release Notes

Bug-fix release in the 2.4.x series.

This release provides improved tolerance (and debugging output) for incomplete fieldmap inputs.

Changes

• FIX: Log incomplete fieldmaps, rather than erroring (#341)
• ENH: Consistently log failures to form fieldmaps (#343

- Python
Published by effigies about 3 years ago

sdcflows - 2.4.0

Release Notes

New feature release in the 2.4.x series.

This release supports fMRIPrep 23.0.x and Nibabies 23.1.x.

Changes

• FIX: Reorient phase-encoding directions along with fieldmaps when preparing inputs to TOPUP (#339)
• FIX: Correct overly-sensitive obliqueness check (#335)

- Python
Published by effigies about 3 years ago

sdcflows - 2.3.0

Release Notes

New feature release in the 2.3.x series.

This release supports fMRIPrep 23.0.x and Nibabies 23.0.x.

Changes

• ENH: Calculate fieldwarps in reference space in unwarp_wf (#334)
• TEST: Squeeze image before passing to SimpleBeforeAfter (#337)
• MAINT: Rotate CircleCI secrets and setup up org-level context (#329)
• CI: Run unit tests on Python 3.10 (#326)
• CI: Switch to miniconda setup, install fsl tools through conda (#322)

- Python
Published by effigies about 3 years ago

sdcflows - 2.2.2

Release Notes

Patch release in the 2.2.x series.

This release resolves a bug affecting some oblique datasets.

What's Changed

• DOC: Add a notebook about susceptibility distortions by @oesteban in https://github.com/nipreps/sdcflows/pull/285
• RF: Generate the b-spline design matrix directly for efficiency by @effigies in https://github.com/nipreps/sdcflows/pull/324

Full Changelog: https://github.com/nipreps/sdcflows/compare/2.2.1...2.2.2

- Python
Published by effigies over 3 years ago

sdcflows - 2.2.1

Release Notes

Patch release in the 2.2.x series.

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

Changes

• ENH: Dynamically choose number of resampling threads to adapt to memory constraints (https://github.com/nipreps/sdcflows/pull/321)

- Python
Published by mgxd over 3 years ago

sdcflows - 2.2.0

Release Notes

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.

Note: SDCFlows drops Python 3.7 starting with 2.2.x series.

Changes

• 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)

- Python
Published by effigies over 3 years ago

sdcflows - 2.1.1

Release Notes

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

Changes

• FIX: Relax tolerance for different affines when concatenating blips (https://github.com/nipreps/sdcflows/pull/265)

- Python
Published by mgxd almost 4 years ago

sdcflows - 2.1.0

Release Notes

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

Changes

• ENH: Add optional session distinction to wrangler (https://github.com/nipreps/sdcflows/pull/261)
• FIX: Align centers of mass, rather than origins (https://github.com/nipreps/sdcflows/pull/253)
• MAINT: Loosen installation restrictions (https://github.com/nipreps/sdcflows/pull/269)

- Python
Published by mgxd about 4 years ago

sdcflows - 2.0.13

Release Notes

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

Changes

• FIX: Relax tolerance for different affines when concatenating blips by @effigies in https://github.com/nipreps/sdcflows/pull/265

Full Changelog: https://github.com/nipreps/sdcflows/compare/2.0.12...2.0.13

- Python
Published by effigies about 4 years ago

sdcflows - 2.0.11

Release Notes

Patch release in the 2.0.x series. Re-enables single EPI fieldmap processing.

Changes

• FIX: Create one fieldmap estimator per EPI-IntendedFor pair (https://github.com/nipreps/sdcflows/pull/258)
• DOCKER: Build with FSL 6 (https://github.com/nipreps/sdcflows/pull/254)

- Python
Published by mgxd over 4 years ago

sdcflows - 2.0.10

Release Notes

Patch release in the 2.0.x series.

Changes

• FIX: Update boilerplate ordering directives (https://github.com/nipreps/sdcflows/pull/229)
• FIX: ishandling of topup coefficients with higher resolution EPIs (https://github.com/nipreps/sdcflows/pull/251)

- Python
Published by mgxd over 4 years ago

sdcflows - 2.0.9

Release Notes

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

Changes

• DOC: Bring implementation details to the foreground of documentation (#248)
• FIX: Implement B0FieldIdentifier / B0FieldSource (#247)

- Python
Published by mgxd over 4 years ago

sdcflows - 2.0.8

Release Notes

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

CHANGES

• FIX: SDC-SyN ("fieldmap-less") overhaul (#239)
• DOC: Self-hosted & multiversion documentation overhaul (#243)
• MAINT: Standardization of containers across NiPreps (#240)

Full Changelog: https://github.com/nipreps/sdcflows/compare/2.0.7...2.0.8

Maintainers

@oesteban

- Python
Published by oesteban over 4 years ago

sdcflows - 2.0.7

Release Notes

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

CHANGES

• 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)

Maintainers

@oesteban, @mgxd, @effigies.

- Python
Published by oesteban over 4 years ago

sdcflows - 2.0.6

Release Notes

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

Changes

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

- Python
Published by mgxd almost 5 years ago

sdcflows - 2.0.5

Release Notes

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

Changes

• FIX: The calculated displacements field not exposed by unwarp workflow (#224)
• MAINT: Use keys.openpgp.org over sks-keyservers (#223)

- Python
Published by mgxd almost 5 years ago

sdcflows - 2.0.4

Release Notes

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

CHANGES

• 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)

- Python
Published by oesteban about 5 years ago

sdcflows - 2.0.3

Release Notes

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

CHANGES

• 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)

- Python
Published by oesteban about 5 years ago

sdcflows - 2.0.2.post1

- Python
Published by oesteban about 5 years ago

sdcflows - 2.0.2

Release Notes

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 B₀ fieldmap unwarping object which is compatible with NiTranforms and evades the problem of fiddling with the target image's x-forms.

CHANGES

• 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: B₀ 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)

- Python
Published by oesteban about 5 years ago

sdcflows - 2.0.1

- Python
Published by oesteban over 5 years ago

sdcflows - 2.0.0

Release Notes

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 (sdcflows.fieldmaps.FieldmapFile and sdcflows.fieldmaps.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. sdcflows.fieldmaps.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 sdcflows.workflows.base.init_fmap_preproc_wf, leveraging sdcflows.fieldmaps.FieldmapEstimation objects.
• Separated out a new utilities module sdcflows.utils for the manipulation of phase information and EPI (echo-planar imaging) 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.

CHANGES

• 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.

- Python
Published by oesteban over 5 years ago

sdcflows - 2.0.0rc5

- Python
Published by oesteban over 5 years ago

sdcflows - 2.0.0rc4

- Python
Published by oesteban over 5 years ago

sdcflows - 2.0.0rc3

- Python
Published by oesteban over 5 years ago

sdcflows - 2.0.0rc2

- Python
Published by oesteban over 5 years ago

sdcflows - 2.0.0rc1

- Python
Published by oesteban over 5 years ago

sdcflows - 1.3.3

Release Notes

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.

- Python
Published by oesteban almost 6 years ago

sdcflows - 1.3.2

Release Notes

Bug-fix release in 1.3.x series.

CHANGES

• FIX: Replace NaNs in fieldmap atlas with zeros (#104)
• ENH: Return out_warp == "identity" if no SDC is applied (#108)

- Python
Published by oesteban almost 6 years ago

sdcflows - 1.3.1

Release Notes

Bug-fix release adapting to use newly refacored DerivativesDataSink

CHANGES

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

- Python
Published by oesteban about 6 years ago

sdcflows - 1.3.0

Release Notes

Minor release enforcing BIDS-Derivatives labels on dseg file.

CHANGES

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

- Python
Published by mgxd about 6 years ago

sdcflows - 1.2.3 - Yanked (Do not use)

Release Notes

Bug-fix release enforcing BIDS-Derivatives labels on dseg file.

CHANGES

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

- Python
Published by oesteban about 6 years ago

sdcflows - 1.2.2

Release Notes

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

CHANGES

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

- Python
Published by effigies about 6 years ago

sdcflows - 1.0.6

Release Notes

Bug-fix release to fix phase-difference masking bug in the 1.0.x series.

CHANGES

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

- Python
Published by effigies about 6 years ago

sdcflows - 1.2.1

Release Notes

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

CHANGES

• MAINT: Migrate from versioneer to setuptools_scm (#97)
• MAINT: Flexibilize dependencies -- nipype, niworkflows, pybids (#95)

- Python
Published by oesteban about 6 years ago

sdcflows - 1.2.0

Release Notes

A minor version release containing a bugfix for the phase-difference map massaging that improves robustness. This release is preparation for fMRIPrep 20.0.0.

CHANGES

• FIX: Scale all phase maps to [0, 2pi] range (#88)
• MNT: Fix package tests (#90)
• MNT: Fix circle deployment (#91)

- Python
Published by oesteban over 6 years ago

sdcflows - 1.0.5

Release Notes

Bug-fix release.

CHANGES

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

- Python
Published by effigies over 6 years ago

sdcflows - 1.1.0

Release Notes

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.

- Python
Published by effigies over 6 years ago

sdcflows - 1.0.4

Release Notes

Bug-fix release.

CHANGES

• FIX: Connect SyN outputs whenever SyN is run (#82)
• MNT: Skim Docker image, optimize CircleCI workflow, and reuse cached results (#80)

- Python
Published by effigies over 6 years ago

sdcflows - 1.0.3

Release Notes

A hotfix release preventing downstream dependency collisions on fMRIPrep.

CHANGES

• PIN: niworkflows-1.0.3 (449c2c2)

- Python
Published by oesteban over 6 years ago

sdcflows - 1.0.2

Release Notes

A hotfix release.

CHANGES

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

- Python
Published by oesteban over 6 years ago

sdcflows - 1.0.1

Release Notes

A bugfix release.

CHANGES

• FIX: Flexibly and cheaply select initial PEPOLAR volumes (#75)
• ENH: Phase1/2 - subtract phases before unwrapping (#70)

- Python
Published by oesteban over 6 years ago

sdcflows - 1.0.0

Release Notes

A first stable release after detaching these workflows off from fMRIPrep. With thanks to Matthew Cieslak and Azeez Adebimpe.

CHANGES

• 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)

- Python
Published by oesteban over 6 years ago

sdcflows - 1.0.0rc1

- Python
Published by oesteban over 6 years ago

sdcflows - 0.1.4

Release Notes

A maintenance release to pin niworkflows to version 1.0.0rc1.

- Python
Published by oesteban over 6 years ago

sdcflows - 0.1.3

Release Notes

Adapts SDCflow to the separation of workflows from Nipype 1.

CHANGES

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

- Python
Published by oesteban over 6 years ago

sdcflows - 0.1.2

BAD RELEASE - DO NOT USE

- Python
Published by oesteban over 6 years ago

sdcflows - 0.1.1

Release Notes

Minor fixup of the infrastructure for deployment from CircleCI

CHANGES

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

- Python
Published by oesteban almost 7 years ago

sdcflows - 0.1.0

Release Notes

First version working with fMRIPrep v1.4.1.

- Python
Published by oesteban almost 7 years ago

sdcflows - 0.0.2

Pin appropriate niworkflows version

- Python
Published by oesteban about 7 years ago

sdcflows - 0.0.1

Moved basic infrastructure and code with history from fMRIPrep

- Python
Published by oesteban about 7 years ago