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Recent Releases of nibabies

nibabies - 25.1.1

Release Notes

A patch release in the 25.1.x series.

Includes a fix to the fieldmap reference orientation to match the B-spline coefficients.

Thanks to @joey-scanga for the contribution!

Changelog

Bug Fixes

  • FIX: Orient fieldmap before checking spline fit (https://github.com/nipreps/nibabies/pull/475)

- Python
Published by mgxd 9 months ago

nibabies - 25.1.0

Release Notes

First release of the 25.1.x series. A few key changes include a new workflow for derivatives compatibility when an anatomical template is not present, and performing a two step registration (currently only for MNI152NLin6Asym) is now the default behavior. This can be disabled by adding --no-multi-step-reg to the command.

Changes

Enhancements

  • ENH: Verify derivatives are compatible with anatomical reference (https://github.com/nipreps/nibabies/pull/459)
  • ENH: Make --multi-step-reg a boolean action, enable by default (https://github.com/nipreps/nibabies/pull/470)
  • ENH: Convert pooch retrieval to interface, allow setting cache dir (https://github.com/nipreps/nibabies/pull/467)

Internals / Maintenance

  • MAINT: bump dependencies, test on python 3.13 (https://github.com/nipreps/nibabies/pull/468)
  • MAINT: deprecate --clean-workdir (https://github.com/nipreps/nibabies/pull/473)

- Python
Published by mgxd 10 months ago

nibabies - 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" (https://github.com/nipreps/nibabies/pull/456)

Enhancements

  • ENH: Add message to show which files are to be used (https://github.com/nipreps/nibabies/pull/452)
  • ENH: Tag anatomical workflows (https://github.com/nipreps/nibabies/pull/463)

Bug Fixes

  • FIX: SyN workflow (https://github.com/nipreps/nibabies/pull/453)
  • FIX: Add Convert3d to Docker image (https://github.com/nipreps/nibabies/pull/461)

Internals / Maintenance

  • MAINT: Support sdcflows@main and smriprep >=0.18 (https://github.com/nipreps/nibabies/pull/462)

- Python
Published by mgxd 11 months ago

nibabies - 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 (https://github.com/nipreps/nibabies/pull/443)

- Python
Published by mgxd about 1 year ago

nibabies - 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 (https://github.com/nipreps/nibabies/pull/437)
    • ENH: Minimize clipping prior to surface reconstruction with MCRIBS (https://github.com/nipreps/nibabies/pull/436)
    • ENH: Output fsLR meshes on subject surfaces (https://github.com/nipreps/nibabies/pull/427)
    • ENH: Add flag for multi-step registration to adult templates (https://github.com/nipreps/nibabies/pull/415) (https://github.com/nipreps/nibabies/pull/425) (https://github.com/nipreps/nibabies/pull/430) (https://github.com/nipreps/nibabies/pull/433)
    • ENH: Option to normalize CSF prior to template registration (https://github.com/nipreps/nibabies/pull/419)
    • ENH: Expand template registration to use either anatomical modality (https://github.com/nipreps/nibabies/pull/418)

  • Bug Fixes

    • FIX: Reduce range that --surface-recon-method auto recommends MCRIBS (https://github.com/nipreps/nibabies/pull/438)
    • FIX: Allow T2 only without the use of --derivatives
    • FIX: New styling catches (https://github.com/nipreps/nibabies/pull/417)
    • FIX: Default surface recon method should be None (https://github.com/nipreps/nibabies/pull/416)

  • Internals / Maintenance

    • TST: Build workflow across different conditions (https://github.com/nipreps/nibabies/pull/409)
    • MAINT: Remove deprecated parser arguments (https://github.com/nipreps/nibabies/pull/407)

- Python
Published by mgxd about 1 year ago

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

- Python
Published by mgxd about 1 year ago

nibabies - 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 (https://github.com/nipreps/nibabies/pull/403)
  • ENH: Add age to session report (https://github.com/nipreps/nibabies/pull/402)
  • ENH: Improvements to age parsing (https://github.com/nipreps/nibabies/pull/395, https://github.com/nipreps/nibabies/pull/398)

Fixes

  • FIX: MCRIBS auto surface reconstruction logic (https://github.com/nipreps/nibabies/pull/399)
  • FIX: Do not force masking of anatomicals when using --derivatives (https://github.com/nipreps/nibabies/pull/400)

Internals / Maintenance

  • MAINT: Revisit warnings filter (https://github.com/nipreps/nibabies/pull/396)
  • MAINT: Automate testing with tox (https://github.com/nipreps/nibabies/pull/404)
  • MAINT: Port over parser arguments and tests from fmriprep (https://github.com/nipreps/nibabies/pull/401)

- Python
Published by mgxd over 1 year ago

nibabies - 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 (https://github.com/nipreps/nibabies/pull/385)
  • DOC: Reformat abbreviations (https://github.com/nipreps/nibabies/pull/386)

- Python
Published by mgxd over 1 year ago

nibabies - 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 fixmultisource_name (https://github.com/nipreps/nibabies/pull/365)
  • FIX: Avoid retrieving multiple templates from latest TF (https://github.com/nipreps/nibabies/pull/353)
  • FIX: Raise informative error if no t1w or t2w found (https://github.com/nipreps/nibabies/pull/347)
  • FIX: Easier pyenv usage (https://github.com/nipreps/nibabies/pull/342)
  • FIX: Catch nonexistent derivatives, clean up subworkflow logic (https://github.com/nipreps/nibabies/pull/336)
  • FIX: Use fsLR reg sphere for MCRIBS morphometrics resampling (https://github.com/nipreps/nibabies/pull/334)
  • FIX: T2star map MNI scaling (https://github.com/nipreps/nibabies/issues/320)

Enhancements

  • ENH: Alter outputs when MCRIBS reconstruction is used (https://github.com/nipreps/nibabies/pull/329)
  • ENH: Use nireports for Report generation + add reportlet per reconstruction (https://github.com/nipreps/nibabies/pull/328)
  • ENH: better repr for Derivatives class (https://github.com/nipreps/nibabies/pull/351)

Refactors

  • RF: Move to fit/apply workflow (https://github.com/nipreps/nibabies/pull/360)
  • RF: Replace resource_filename with load_data (https://github.com/nipreps/nibabies/pull/345)

Maintenance

  • MAINT: Bump urllib3 from 2.0.3 to 2.0.7 (https://github.com/nipreps/nibabies/pull/319)
  • MAINT: Raise minimum to 3.10, bump actions (https://github.com/nipreps/nibabies/pull/337)
  • MAINT: Bump pillow from 9.5.0 to 10.0.1 (https://github.com/nipreps/nibabies/pull/317)
  • MAINT: Update to latest migas API (https://github.com/nipreps/nibabies/pull/326)

Documentation

  • DOC: Use correct argument flag (https://github.com/nipreps/nibabies/pull/338)
  • DOC: Move to new theme, add outputs description (https://github.com/nipreps/nibabies/pull/383)

- Python
Published by mgxd over 1 year ago

nibabies - 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 (https://github.com/nipreps/nibabies/pull/376)
  • FIX: Ensure 2mm template is added when running CIFTI (https://github.com/nipreps/nibabies/pull/381)
  • CI: Fix smoke tests (https://github.com/nipreps/nibabies/pull/379)
  • FIX: Do not require mniinfant xfm if no cifti (https://github.com/nipreps/nibabies/pull/377)

- Python
Published by mgxd over 1 year ago

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

- Python
Published by mgxd over 1 year ago

nibabies - 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 (https://github.com/nipreps/nibabies/pull/326)
  • FIX: T2star map MNI scaling (https://github.com/nipreps/nibabies/issues/320)
  • ENH: Alter outputs when MCRIBS reconstruction is used (https://github.com/nipreps/nibabies/pull/329)
  • ENH: Use nireports for Report generation + add reportlet per reconstruction (https://github.com/nipreps/nibabies/pull/328)

- Python
Published by mgxd over 2 years ago

nibabies - 23.1.0

Release Notes

The next minor release of NiBabies, this release includes a number of new goodies, including:

New Surface Reconstruction

M-CRIB-S (Adamson et al.), has shown to improve performance in participants under 9 months. If you would like to try this method, add the following to your command: --surface-recon-method mcribs.

*Currently, a T2w image and pre-computed segmentation derivative must be provided to run mcribs.

Improved batch processing

NiBabies now automatically parses the BIDS directory for participant ages, first searching in the participant's session.tsv, and falling back to participants.tsv. This simplifies batch submissions including multiple subjects & sessions. As a result, the --age-months flag has been deprecated, and will be removed in a later release.

Goodvoxels projection

An option to determine and exclude high-variance voxels from being projected to the surface when creating CIFTI files. To enable this, add --project-goodvoxels to your command.

Single anatomical processing

Running NiBabies is now less restrictive, and will still process data missing either a T1w / T2w image. However, for best results, it is recommended to collect and include both for processing.

Anat-specific derivatives inputs

Previous, NiBabies expected input from the --derivatives flag to be in T1w space, using the entity space-orig. This has now been changed to support derivatives in either T1w or T2w space. For more information, please see https://nibabies.readthedocs.io/en/23.1.0/faqs.html#leveraging-precomputed-results

Changelog

  • CI: Purge codecov python package (https://github.com/nipreps/nibabies/pull/282)
  • DKR: Upgrade Docker base, c3d (https://github.com/nipreps/nibabies/pull/275)
  • DKR: Add M-CRIB-S to Docker container (https://github.com/nipreps/nibabies/pull/283)
  • DKR: Update dependencies, split into multi-stage build
  • ENH: Add option to exclude projecting high variance voxels to surface (https://github.com/nipreps/nibabies/pull/278)
  • ENH: Resample morphometrics to fsLR CIFTI-2 files when outputing CIFTIs (https://github.com/nipreps/nibabies/pull/279)
  • ENH: Add MCRIBReconAll as alternative surface reconstruction method (https://github.com/nipreps/nibabies/pull/283)
  • ENH: Reorder anatomical processsing, run ANTs DenoiseImage on anatomicals (https://github.com/nipreps/nibabies/pull/286)
  • ENH: Extract participant ages from BIDS sources, deprecate --age-months (https://github.com/nipreps/nibabies/pull/287)
  • ENH: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2star map estimation (https://github.com/nipreps/nibabies/pull/296)
  • ENH: Allow precomputed derivatives in T1w or T2w space (https://github.com/nipreps/nibabies/pull/305)
  • ENH: Add separate workflow for single anatomical processing (https://github.com/nipreps/nibabies/pull/316)
  • FIX: Improve free memory estimation (https://github.com/nipreps/nibabies/pull/284)
  • FIX: Ensure age is extracted from sessions file (https://github.com/nipreps/nibabies/pull/291)
  • FIX: Restore CIFTI medial wall masking, subcortical volume LAS reorientation (https://github.com/nipreps/nibabies/pull/298)
  • FIX: Recify "goodvoxels" surface projection (https://github.com/nipreps/nibabies/pull/301)
  • FIX: Connect derivatives mask to mcribs recon (https://github.com/nipreps/nibabies/pull/323)
  • MAINT: Drop TemplateFlowSelect patches (https://github.com/nipreps/nibabies/pull/290)

- Python
Published by mgxd over 2 years ago

nibabies - 23.1.0 release candidate 1

The next minor release of NiBabies, this release includes a number of new goodies, including:

New surface reconstruction option

M-CRIB-S (Adamson et al., https://www.nature.com/articles/s41598-020-61326-2), has shown to improve performance in participants under 9 months. If you would like to try this method, add the following to your command: --surface-recon-method mcribs.

Note: Currently, a T2w image and pre-computed segmentation derivative must be provided to run mcribs.

Improved batch processing

NiBabies now automatically parses the BIDS directory for participant ages, first searching in the participant's session.tsv, and falling back to participants.tsv. This simplifies batch submissions including multiple subjects & sessions. As a result, the --age-months flag has been deprecated, and will be removed in a later release.

Goodvoxels projection

An option to determine and exclude high-variance voxels from being projected to the surface when creating CIFTI files. To enable this, add --project-goodvoxels to your command.

Single anatomical processing

Running NiBabies is now less restrictive, and will still process data missing either a T1w / T2w image. However, for best results, it is recommended to collect and include both for processing.

Full Changelog

  • CI: Purge codecov python package (#282)
  • DKR: Upgrade Docker base, c3d (#275)
  • DKR: Add M-CRIB-S to Docker container (#283)
  • DKR: Update dependencies, split into multi-stage build
  • ENH: Add option to exclude projecting high variance voxels to surface (#278)
  • ENH: Resample morphometrics to fsLR CIFTI-2 files when outputing CIFTIs (#279)
  • ENH: Add MCRIBReconAll as alternative surface reconstruction method (#283)
  • ENH: Reorder anatomical processsing, run ANTs DenoiseImage on anatomicals (#286)
  • ENH: Extract participant ages from BIDS sources, deprecate --age-months (#287)
  • ENH: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2star map estimation (#296)
  • ENH: Allow precomputed derivatives in T1w or T2w space (#305)
  • ENH: Add separate workflow for single anatomical processing (#316)
  • FIX: Improve free memory estimation (#284)
  • FIX: Ensure age is extracted from sessions file (#291)
  • FIX: Restore CIFTI medial wall masking, subcortical volume LAS reorientation (#298)
  • FIX: Recify "goodvoxels" surface projection (#301)
  • MAINT: Drop TemplateFlowSelect patches (#290)

- Python
Published by mgxd over 2 years ago

nibabies - 23.1.0 release candidate 0

Release Notes

A release candidate of the next minor release of NiBabies, this release includes a number of new goodies, including:

New surface reconstruction option

M-CRIB-S (Adamson et al., https://www.nature.com/articles/s41598-020-61326-2), has shown to improve performance in participants under 9 months. If you would like to try this method, add the following to your command: --surface-recon-method mcribs.

Note: Currently, a pre-computed segmentation derivative must be provided to run mcribs.

Improved batch processing

NiBabies now automatically parses the BIDS directory for participant ages, first searching in the participant's session.tsv, and falling back to participants.tsv. This simplifies batch submissions including multiple subjects & sessions. As a result, the --age-months flag has been deprecated, and will be removed in a later release.

Augmented surface projection

An option to determine and exclude high-variance voxels from being projected to the surface when creating CIFTI files. To enable this, add --project-goodvoxels to your command.

  • CI: Purge codecov python package (https://github.com/nipreps/nibabies/pull/282)
  • DKR: Upgrade Docker base, c3d (https://github.com/nipreps/nibabies/pull/275)
  • DKR: Add M-CRIB-S to Docker container (https://github.com/nipreps/nibabies/pull/283)
  • DKR: Update dependencies, split into multi-stage build
  • ENH: Add option to exclude projecting high variance voxels to surface (https://github.com/nipreps/nibabies/pull/278)
  • ENH: Resample morphometrics to fsLR CIFTI-2 files when outputing CIFTIs (https://github.com/nipreps/nibabies/pull/279)
  • ENH: Add MCRIBReconAll as alternative surface reconstruction method (https://github.com/nipreps/nibabies/pull/283)
  • ENH: Reorder anatomical processsing, run ANTs DenoiseImage on anatomicals (https://github.com/nipreps/nibabies/pull/286)
  • ENH: Extract participant ages from BIDS sources, deprecate --age-months (https://github.com/nipreps/nibabies/pull/287)
  • ENH: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2star map estimation (https://github.com/nipreps/nibabies/pull/296)
  • FIX: Improve free memory estimation (https://github.com/nipreps/nibabies/pull/284)
  • FIX: Ensure age is extracted from sessions file (https://github.com/nipreps/nibabies/pull/291)
  • FIX: Restore CIFTI medial wall masking, subcortical volume LAS reorientation (https://github.com/nipreps/nibabies/pull/298)
  • FIX: Recify "goodvoxels" surface projection (https://github.com/nipreps/nibabies/pull/301)
  • MAINT: Drop TemplateFlowSelect patches (https://github.com/nipreps/nibabies/pull/290)

- Python
Published by mgxd over 2 years ago

nibabies - 23.0.0

Release Notes

New year, new NiBabies minor series! Some of the highlights of this release include: - New run-wise BOLD reference generation, prioritizing single-band references if available, unless avoided with the --ignore sbrefs flag. - New output: Preprocessed T2w in T1w space.

A full list of changes can be found below.

Changes

  • ENH: Runwise bold reference generation (#268)
  • ENH: Add preprocessed T2w volume to outputs (#271)
  • MAINT: Drop versioneer for hatch backend, fully embrace pyproject.toml (#265)
  • MAINT: Rotate CircleCI secrets and setup up org-level context (#266)
  • CI: Bump convenience images, limit datalad (#267)
  • FIX: Remove legacy CIFTI variant support (#264)

- Python
Published by mgxd about 3 years ago

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

- Python
Published by mgxd over 3 years ago

nibabies - 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 (https://github.com/nipreps/nibabies/pull/233)

- Python
Published by mgxd over 3 years ago

nibabies - 22.1.2

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

- Python
Published by mgxd over 3 years ago

nibabies - 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 (https://github.com/nipreps/nibabies/pull/231)
  • RF: migas reporting (https://github.com/nipreps/nibabies/pull/230)

- Python
Published by mgxd over 3 years ago

nibabies - 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 (https://github.com/nipreps/nibabies/pull/223)
  • FIX: Vastly improve multi-echo handling (https://github.com/nipreps/nibabies/pull/220)
  • ENH: Add option to use recon-all instead of infantreconall (https://github.com/nipreps/nibabies/pull/214)
  • ENH: Add migas telemetry to nibabies (https://github.com/nipreps/nibabies/pull/226)
  • ENH: Add interface for reorienting images (https://github.com/nipreps/nibabies/pull/229)
  • DOCKER: Bump Python to 3.9 (https://github.com/nipreps/nibabies/pull/221)
  • RF/ENH: Rework workflow generation (https://github.com/nipreps/nibabies/pull/219)

- Python
Published by mgxd over 3 years ago

nibabies - 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)

- Python
Published by mgxd almost 4 years ago

nibabies - 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)

- Python
Published by mgxd almost 4 years ago

nibabies - 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)

- Python
Published by mgxd almost 4 years ago

nibabies - 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 (https://github.com/nipreps/nibabies/pull/203)
  • ENH: Improve fieldmap support (https://github.com/nipreps/nibabies/pull/205)
  • MAINT: Bump niworkflows (https://github.com/nipreps/nibabies/pull/208)
  • STY: Bump style dependencies, run isort on repo (https://github.com/nipreps/nibabies/pull/206)

- Python
Published by mgxd about 4 years ago

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

- Python
Published by mgxd about 4 years ago

nibabies - 22.0.0 release candidate 1

Changes

  • DOC: Add FAQs page (https://github.com/nipreps/nibabies/pull/164)
  • ENH: Add --me-output-echos CLI flag (https://github.com/nipreps/nibabies/pull/174)
  • ENH: Precomputed derivatives (https://github.com/nipreps/nibabies/pull/173)
  • ENH: Validate files passed with --derivatives (https://github.com/nipreps/nibabies/pull/182)
  • FIX: Check if segmentation directory exists (https://github.com/nipreps/nibabies/pull/165)
  • FIX: Update report spec to reflect infant_recon_all (https://github.com/nipreps/nibabies/pull/167)
  • FIX: ICA Aroma imports (https://github.com/nipreps/nibabies/pull/170)
  • FIX: Relabel sub-structures before discarding (https://github.com/nipreps/nibabies/pull/186)
  • FIX: Use precomputed aseg within infant_recon_all (https://github.com/nipreps/nibabies/pull/184)
  • FIX: Remove excess arguments on wrapper tests (https://github.com/nipreps/nibabies/pull/181)
  • MAINT: Add missing toml dependency (f9c26bc41143fa8889d93f2119e254cfdf7e71a4)
  • MAINT: Add pre-commit checks (https://github.com/nipreps/nibabies/pull/178)
  • MAINT: Add RTD config (https://github.com/nipreps/nibabies/pull/173)
  • MAINT: Freeze black version (https://github.com/nipreps/nibabies/pull/185)
  • RF: Wrapper usage logic (https://github.com/nipreps/nibabies/pull/183)
  • STY/TEST: Set global style and doctest options (https://github.com/nipreps/nibabies/pull/162)

- Python
Published by mgxd about 4 years ago

nibabies - 21.0.2

Release Notes

A patch release in the 21.0.x series. This release removes the 24 month age cap for infant recon all processing, as well as includes various small maintenance fixes.

Changelog

  • DOC: Use dynamic versioning for examples (#151)
  • ENH: Remove infant recon all age cap (#154)
  • FIX: Generate boilerplate (#157)
  • FIX: Avoid requiring service when checking wrapper version (#159)
  • ~MAINT: Fix dirty version on release (#144)~
  • MAINT: Only alter pybids config in legacy versions (#152)
  • MAINT: Prefetch neonate MNIInfant templates (#159)
  • MAINT: Update git-annex version (#159)
  • RF: Initialize BIDSLayout with dedicated indexer (#146)

- Python
Published by mgxd over 4 years ago

nibabies - 21.0.1

Release Notes

A patch release in the 21.0.x series.

This patch release is for all Docker/Singularity users.

infant_recon_all did not have access to all required templates, causing failures for certain ages.

Changes

  • DOCKER: Add missing infant_recon_all templates (130dcf3)

- Python
Published by mgxd over 4 years ago

nibabies - 21.0.0

Release Notes

The first major release series of 2021.

This release includes enhancements, such as: - Fine-grain subcortical alignment during CIFTI generation - Improved functional registration to template space - Greatly minimized container environment

Additionally, a plethora of bug-fixes are included, and documentation has been improved.

As with all minor version increments, working directories from previous versions should not be reused.

If you encounter any issues with this release, please let us know by posting an issue on our GitHub page!

Changes

  • DOC: Set up external readthedocs documentation (#119) (#126) (#128)
  • DOCKER: Reduce container image size (#105) (#133)
  • DOCKER: Strip ABI tag from libQt5Core.so.5 (#109)
  • DOCKER: Modernize Dockerfile (#85)
  • ENH: Port slice timing correction enhancements from fMRIPrep (#137)
  • ENH: Change default --output-layout to bids (#130)
  • ENH: Subcortical alignment workflow (#72)
  • ENH: Framewise displacement head radius flag (#104)
  • ENH: Incorporate subcortical CIFTI alignment to functional processing (#102)
  • ENH: Do not run infantreconall if already completed (#101)
  • FIX: Handle sessions when grouping BOLDs (#139)
  • FIX: Ensure MNIInfant is added if no --output-spaces are used (#136)
  • FIX: Ensure nibabies-wrapper patches are correctly bound (#113)
  • FIX: BOLD to template normalization (#99)
  • FIX: SDC fieldwarp application (#98)
  • FIX: Avoid running BBReg under certain conditions (#95)
  • FIX: Standard output spaces (#92)
  • FIX: Small Docker environment fixes (#86)
  • FIX: Feed NiTransforms with LTAs of type RAS2RAS (#84)
  • MAINT: Rename default infant_recon_all output directory (#129)
  • MAINT: Bump SDCFlows to latest bugfix version (d799fee)
  • MAINT: Attempt to pull most recent dev version (#94)
  • MAINT: Initial CircleCI workflow (#93)
  • STY: black nibabies module (#118)

- Python
Published by mgxd over 4 years ago

nibabies - 0.1.2 Hotfix Release

Release Notes

This release fixes an issue with the BOLD reference grouping logic potentially processing the same BOLD file twice, leading to a duplication error.

Changes

  • FIX: BOLD file duplication error (#83)

- Python
Published by mgxd almost 5 years ago

nibabies - 0.1.1

Release Notes

Summer is here and so is another NiBabies release 🌞 !* This release fixes up issues with BIDS validation, as well as includes a wrapper script to facilitate running with either Docker or Singularity. The wrapper can be installed through pip, like so:

pip install nibabies-wrapper==0.1.1

Check out the full changelog below.

Changes

  • FIX: BIDS validation error
  • ENH: Additional wrapper script (nibabies-wrapper) to facilitate running through Docker/Singularity
  • DOC: Updates anatomical processing figure, adds functional processing figure
  • DOC: Fixes typo in README usage

* Sorry southern hemisphere users ☃️

- Python
Published by mgxd almost 5 years ago

nibabies - 0.1.0

0.1.0 (May 26, 2021)

This minor release includes support for both anatomical and functional preprocessing.

  • Implements susceptibility distortion correction for BOLDs
  • Improved documentation
  • Adds estimated fieldmap report
  • Removed unused commandline arguments

- Python
Published by mgxd almost 5 years ago