Releases: nipreps/nibabies
24.0.1
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
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
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
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_filenamewithload_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.
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 (#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)
- FIX: Connect derivatives mask to mcribs recon (#323)
- MAINT: Drop TemplateFlowSelect patches (#290)
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)
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 (#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)
- 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)
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 sbrefsflag. - 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)
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)