25.0.2

Release Notes

A patch release including a couple key bug fixes:

• Adds missing dependency to Docker image when BOLD coregistration falls back to FSL
• Fixes connections to allow fieldmap-less SDC

Thanks to @joey-scanga for the contribution!

Changes

Documentation

• DOC: Changed "B0Identifier" -> "B0FieldIdentifier" (#456)

Enhancements

• ENH: Add message to show which files are to be used (#452)
• ENH: Tag anatomical workflows (#463)

Bug Fixes

• FIX: SyN workflow (#453)
• FIX: Add Convert3d to Docker image (#461)

Internals / Maintenance

• MAINT: Support sdcflows@main and smriprep >=0.18 (#462)

25.0.1

Release Notes

A bug-fix release to address an issue when using a precomputed mask for MCRIBS surface reconstruction without an anatomical template.

Changelog

• FIX: Match mask header prior to n4 correction (#443)

25.0.0

Release Notes

A new minor release with improvements to anatomical to template spatial normalization.

Registration will now prioritize the same modality as the anatomical template, if available.

A new flag --norm-csf performs CSF normalization on the anatomical template prior to template registration.

A new flag --multi-step-reg adds an intermediate step when registering to MNI152NLin6Asym, first performing anatomical -> MNIInfant:cohort-X (age matched by default), and then concatenates the transform with an already computed MNIInfant -> MNI152NLin6Asym.

Both of the new flags above are disabled by default, but have shown promise and may become defaults in the next release. Please experiment with your data, and any feedback on the results would be greatly appreciated!

With thanks to @mattcieslak and @tsalo

Changelog

• Enhancements

  • ENH: Output anatomical coregistration transform + report (#437)
  • ENH: Minimize clipping prior to surface reconstruction with MCRIBS (#436)
  • ENH: Output fsLR meshes on subject surfaces (#427)
  • ENH: Add flag for multi-step registration to adult templates (#415) (#425) (#430) (#433)
  • ENH: Option to normalize CSF prior to template registration (#419)
  • ENH: Expand template registration to use either anatomical modality (#418)

• Bug Fixes

  • FIX: Reduce range that --surface-recon-method auto recommends MCRIBS (#438)
  • FIX: Allow T2 only without the use of --derivatives
  • FIX: New styling catches (#417)
  • FIX: Default surface recon method should be None (#416)

• Internals / Maintenance

  • TST: Build workflow across different conditions (#409)
  • MAINT: Remove deprecated parser arguments (#407)

25.0.0 Release Candidate 1

Release Notes

A release candidate for a new minor version with improvements to anatomical to template spatial normalization.

Registration will now prioritize the same modality as the anatomical template, if available.

A new flag --norm-csf performs normalization on the lower bound of CSF values prior to template registration.

A new flag --multi-step-reg adds an intermediate step when registering to MNI152NLin6Asym, first performing anatomical -> MNIInfant:cohort-X (age matched by default), and then concatenates the transform with an already computed MNIInfant -> MNI152NLin6Asym.

Both of these flags are experimental and disabled unless requested, but comparisons and feedback with your data are helpful for future determinations!

Changes

• ENH: Output anatomical coregistration transform + report (#437)
• ENH: Minimize clipping prior to surface reconstruction with MCRIBS (#436)
• ENH: Output fsLR meshes on subject surfaces (#427)
• ENH: Add flag for multi-step registration to adult templates (#415) (#425) (#430) (#433)
• ENH: Option to normalize CSF prior to template registration (#419)
• ENH: Expand template registration to use either anatomical modality (#418)
• FIX: Reduce range that --surface-recon-method auto recommends MCRIBS (#438)
• FIX: Allow T2 only without the use of --derivatives
• FIX: New styling catches (#417)
• FIX: Default surface recon method should be None (#416)
• TST: Build workflow across different conditions (#409)
• MAINT: Remove deprecated parser arguments (#407)

24.1.0

Release Notes

This new minor release includes a few bug fixes, such as excluding MCRIBS from surface reconstruction without a precomputed segmentation and ensuring generated derivatives are not masked, as well as improvements to reporting.

Changelog

Enhancements

• ENH: Add boilerplate, errors to report (#403)
• ENH: Add age to session report (#402)
• ENH: Improvements to age parsing (#395, #398)

Fixes

• FIX: MCRIBS auto surface reconstruction logic (#399)
• FIX: Do not force masking of anatomicals when using --derivatives (#400)

Internals / Maintenance

• MAINT: Revisit warnings filter (#396)
• MAINT: Automate testing with tox (#404)
• MAINT: Port over parser arguments and tests from fmriprep (#401)

24.0.1

Release Notes

A patch release with a fix for the BOLD T2* workflow. The command line argument --me-t2s-fit-method was added for finer control when processing multi-echo datasets.

Changelog

• FIX: Add missing me-t2s-fit-method option (#385)
• DOC: Reformat abbreviations (#386)

24.0.0

Release Notes

This major release includes a substantial refactoring of the pipeline.

One key addition is the addition of the --level flag, which can take the arguments minimal, resampling or full. The default is full, which should produce nearly the same results as previous versions. minimal will produce only the minimum necessary to deterministically generate the remaining derivatives. resampling will produce some additional derivatives, intended to simplify resampling with other tools.

The --derivatives flag was altered to take arguments in the form name=/path/to/dir.
For each directory provided, if a derivative is found - it will be used instead of computing it from scratch. If a derivative is not found, NiBabies will compute it and proceed as usual.

Taken together, these features can allow a dataset provider to run a minimal NiBabies run, targeting many output spaces, while a user can then run a --derivatives run to generate additional derivatives in only the output spaces they need. Another use case is to provide an precomputed derivative to override the default NiBabies behavior, enabling easier workarounds for bugs or experimentation with alternatives.

Another new feature is a dynamic anatomical reference, which is set based on surface reconstruction method or through the --reference-anatomical flag. Previously, T1w was the default output space. Now, the reference anatomical is determined based on the surface reconstruction method.

Additionally, minor adjustments have been made to MCRIBS surface reconstruction to address failure rates. This is still an on-going investigation, but preliminary results look promising.

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. To disable Jacobian weighting, add fmap-jacobian to the --ignore argument.

Finally, a new resampling method has been added, to better account for susceptibility distortion and motion in a single shot resampling to a volumetric target space. We anticipate extending this to surface targets in the future.

Changelog

Fixes

• FIX: nest pathlib import in fix_multi_source_name (#365)
• FIX: Avoid retrieving multiple templates from latest TF (#353)
• FIX: Raise informative error if no t1w or t2w found (#347)
• FIX: Easier pyenv usage (#342)
• FIX: Catch nonexistent derivatives, clean up subworkflow logic (#336)
• FIX: Use fsLR reg sphere for MCRIBS morphometrics resampling (#334)
• FIX: T2star map MNI scaling (#320)

Enhancements

• ENH: Alter outputs when MCRIBS reconstruction is used (#329)
• ENH: Use nireports for Report generation + add reportlet per reconstruction (#328)
• ENH: better repr for Derivatives class (#351)

Refactors

• RF: Move to fit/apply workflow (#360)
• RF: Replace resource_filename with load_data (#345)

Maintenance

• MAINT: Bump urllib3 from 2.0.3 to 2.0.7 (#319)
• MAINT: Raise minimum to 3.10, bump actions (#337)
• MAINT: Bump pillow from 9.5.0 to 10.0.1 (#317)
• MAINT: Update to latest migas API (#326)

Documentation

• DOC: Use correct argument flag (#338)
• DOC: Move to new theme, add outputs description (#383)

24.0.0 Second Release Candidate

Release Notes

The second RC of the 24.0.x series. This releases fixes a few issues, adds support for parsing age from scans.tsv files, and will convert years and weeks units into months.

Changelog

• ENH: Require units when age parsing, ingest scans.tsv (#376)
• FIX: Ensure 2mm template is added when running CIFTI (#381)
• CI: Fix smoke tests (#379)
• FIX: Do not require mniinfant xfm if no cifti (#377)

24.0.0 Release Candidate 0

Release Notes

This major release includes a substantial refactoring of the pipeline.

One key addition is the addition of the --level flag, which can take the arguments minimal, resampling or full. The default is full, which should produce nearly the same results as previous versions. minimal will produce only the minimum necessary to deterministically generate the remaining derivatives. resampling will produce some additional derivatives, intended to simplify resampling with other tools.

The --derivatives flag was altered to take arguments in the form name=/path/to/dir.
For each directory provided, if a derivative is found - it will be used instead of computing it from scratch. If a derivative is not found, NiBabies will compute it and proceed as usual.

Taken together, these features can allow a dataset provider to run a minimal NiBabies run, targeting many output spaces, while a user can then run a --derivatives run to generate additional derivatives in only the output spaces they need. Another use case is to provide an precomputed derivative to override the default NiBabies behavior, enabling easier workarounds for bugs or experimentation with alternatives.

Another new feature is a dynamic anatomical reference, which is set based on surface reconstruction method or through the --reference-anatomical flag. Previously, T1w was the default output space.

Additionally, minor adjustments have been made to MCRIBS surface reconstruction to address failure rates. This is still an on-going investigation, but preliminary results look promising.

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. To disable Jacobian weighting, add fmap-jacobian to the --ignore argument.

Finally, a new resampling method has been added, to better account for susceptibility distortion and motion in a single shot resampling to a volumetric target space. We anticipate extending this to surface targets in the future.

Changes

• RF: Move to fit/apply workflow (#360)
• FIX: nest pathlib import in fix_multi_source_name (#365)
• FIX: Avoid retrieving multiple templates from latest TF (#353)
• ENH: better repr for Derivatives class (#351)
• FIX: Raise informative error if no t1w or t2w found (#347)
• Replace resource_filename with load_data (#345)
• FIX: Easier pyenv usage (#342)
• Build(deps): Bump urllib3 from 2.0.3 to 2.0.7 (#319)
• Build(deps): Bump pillow from 9.5.0 to 10.0.1 (#317)
• DOC: Use correct argument flag (#338)
• MAINT: Raise minimum to 3.10, bump actions (#337)
• FIX: Catch nonexistent derivatives, clean up subworkflow logic (#336)
• Use fsLR reg sphere for MCRIBS morphometrics resampling (#334)
• FIX: Multiple T2ws, coerce reference to string (#333)

24.0.0 - alpha 1

This preliminary release alters some outputs when using MCRIBS surface reconstruction, as well as updates reports.

• MAINT: Update to latest migas API (#326)
• FIX: T2star map MNI scaling (#320)
• ENH: Alter outputs when MCRIBS reconstruction is used (#329)
• ENH: Use nireports for Report generation + add reportlet per reconstruction (#328)