22.2.0

Release Notes

The final NiBabies minor series of 2022!
Some highlights of the new additions in this release series includes:

• Surface morphometrics outputs, including cortical thickness
• T2star maps for multiecho data, projected to target output spaces

This series will be the last to support Python 3.7.

Changes

• FIX: Remove cortex masking during vol2surf sampling (#258)
• ENH: Improve migas telemetry (#257)
• CI: GitHub actions update (#256)
• ENH: Add morphometric outputs (#255)
• ENH: Output T2star maps for multiecho data (#252)
• FIX: Use the binarized output from the brain extraction (#246)
• DOC: Add long description including background/significance (#243)
• CI: Fix docker credential error (#244)
• DOC: Advertise nipreps community pages, add section on contributions (#242)

22.1.3

Release Notes

This patch release includes a vital fix for susceptibility distortion correction on multi-echo data.

Changes

• FIX: Field name for multi-echo fieldmap correction (#233)

22.1.2

This patch release includes a fix to FreeSurfer version detection, which was causing recon-all to use outdated flags.

22.1.1

Release Notes

A bugfix release that includes missing files needed to run infant_recon_all.

Changes

• FIX: Add missing shared object for infant_recon_all (#231)
• RF: migas reporting (#230)

22.1.0

Release Notes

A new minor release! The 22.1.x series of NiBabies includes:

• A new flag (--force-reconall) to use FreeSurfer recon-all instead of infant_recon_all.
• Improved alignment between FreeSurfer outputs and processed anatomical.
• Decreased memory usage while running across multiple processes (default).
• Fix to multi-echo processing in cases where an optimally combined file of all echoes was missing.
• Fix to the subcortical CIFTI to be in LAS orientation.

Changes

• FIX: Correct fsnative <-> anatomical transforms (#223)
• FIX: Vastly improve multi-echo handling (#220)
• ENH: Add option to use recon-all instead of infant_recon_all (#214)
• ENH: Add migas telemetry to nibabies (#226)
• ENH: Add interface for reorienting images (#229)
• DOCKER: Bump Python to 3.9 (#221)
• RF/ENH: Rework workflow generation (#219)

22.1.0 - second release candidate

Release Notes

This release builds off the first release candidate, 22.1.0rc0, and adds a crucial fix to the fsnative <-> anatomical transforms. Additionally, the bbregister workflow has been re-enabled as the default BOLD to structural coregistration, assuming FreeSurfer is being used.

Changes

• FIX: Correct fsnative <-> anatomical transforms (#223)

22.1.0 - first release candidate

Release Notes

A release candidate for the upcoming 22.1.x series.

This release include an update to the workflow generation, temporarily patching OMP_NUM_THREADS to greatly reduce virtual memory accumulation through the workflow. Additionally, multi-echo support has been improved to ensure echos are processed together, and produce an optimally combined preprocessed BOLD output.

Changes

• DOCKER: Bump Python to 3.9 (#221)
• FIX: Vastly improve multi-echo handling (#220)
• RF/ENH: Rework workflow generation (#219)

22.0.2

Release Notes

A bug-fix release in the 22.0.x series.

This release includes a fix to a problem where --cifti-output was not
producing any outputs.

Changes

• CI: Force all git-annex dependencies to be installed (#217)
• CI: Simplify config with anchors (#209)
• FIX: Remedy missing CIFTI outputs (#212)
• MAINT: Set maximum scipy for Python 3.7.x (#216)

22.0.1

Release Notes

A bug-fix release in the 22.0.x series.

This release includes a fix for when using UNCInfant as an output space,
as well as a few improvements to susceptibility distortion correction (SDC).
These include a new flag (--topup-max-vols) for controlling the number of
volumes used by TOPUP, and support for SDC in the case where single phase-encoding
fieldmap is used to correct opposite phase-encoding BOLD/EPI runs.

Warning ⚠️

This release includes a new version of PyBIDS, which now preserves any
zero-padding within the run entity. As a result, NiBabies output naming
may slightly differ from previous versions.

Full Changelog

• CI: Migrate to token auth when uploading to pypi (#203)
• ENH: Improve fieldmap support (#205)
• MAINT: Bump niworkflows (#208)
• STY: Bump style dependencies, run isort on repo (#206)

22.0.0

The first NiBabies release of the year!

The first entry of the 22.0.x series, this release includes a number of new features, as well as various bug fixes. Some of the most notable changes include:

• A new flag --derivatives to allow passing in precomputed derivatives. For more information on how to use this, see the FAQs.
  • Users can now leverage a precomputed brain mask and/or discrete anatomical segmentations.
• A new flag --me-output-echoes to output individual corrected echo time series.
  • This is useful when doing additional multi-echo processing.
• Refinements to CIFTI generation, improve subcortical structure labeling.

Thank you for using NiBabies!

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.

Changelog

• CI: Add workflow smoke tests (#100)
• DOC: Add FAQs page (#164)
• DOCKER: Upgrade to FSL6, use niprep miniconda base layer (#191)
• ENH: Add major/minor version prefix to base workflow name (#202)
• ENH: Add --me-output-echos CLI flag (#174)
• ENH: Precomputed derivatives (#173)
• ENH: Validate files passed with --derivatives (#182)
• FIX: Clean up generated boilerplate (#200)
• FIX: Various Configuration module touch-ups (#197)
• FIX: Clean up default output space handling (#196)
• FIX: Pandoc citeproc API incompatibility (#195)
• FIX: Check if segmentation directory exists (#165)
• FIX: Update report spec to reflect infant_recon_all (#167)
• FIX: ICA Aroma imports (#170)
• FIX: Relabel sub-structures before discarding (#186)
• FIX: Use precomputed aseg within infant_recon_all (#184)
• FIX: Remove excess arguments on wrapper tests (#181)
• MAINT: Update versioneer, allow static versioning (#190)
• MAINT: Ensure version is written to version file (#189)
• MAINT: Add missing toml dependency
• MAINT: Add pre-commit checks (#178)
• MAINT: Add RTD config (#173)
• MAINT: Freeze black version (#185)
• RF: Wrapper usage logic (#183)
• STY/TEST: Set global style and doctest options (#162)