Releases: nipreps/nibabies
25.2.0
Release Notes
The first release of the 25.2.x series.
This release synchronizes with downstream dependencies, as well as
leverages TemplateFlow to retrieve intermediate transforms used during multi-step registration.
If you are reusing a previous TemplateFlow cache (which may be the case if running with
Apptainer / Singularity), you will need to clear or update your cache to ensure these new files
are available.
Thanks to @LuciMoore for the contribution!
Changes
Documentation
- DOC: MCRIBS and surf recon methods chosen based on age (#485)
Enhancements
- ENH: Retrieve transforms with templateflow (#486)
- ENH: Save cortex mask (#487)
- ENH: Add multiverse output layout (#481)
Bug Fixes
- FIX: Default to grid-constant when resampling BOLD to output spaces
- FIX: Propagate error code if pipeline run is unsuccessful
Contributors
Assets 2
25.1.2
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 (#475)
Contributors
Assets 2
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 (#459)
- ENH: Make
--multi-step-rega boolean action, enable by default (#470) - ENH: Convert pooch retrieval to interface, allow setting cache dir (#467)
Internals / Maintenance
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
Bug Fixes
Internals / Maintenance
- MAINT: Support sdcflows@main and smriprep >=0.18 (#462)
Contributors
Assets 2
25.0.1
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
-
Internals / Maintenance
Contributors
Assets 2
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 autorecommends 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)