0.8.0

Release Notes

A new minor release incorporating small iterations and improvements on
NiWorkflows, and including some bug-fixes/enhancements.

Changes

• DOC: Ensure copyright notice is found in all Python files (#248)
• FIX: Revert to FAST for tissue probability segmentations (#263)
• FIX: Sturdier version check of sMRIPrep-wrapper package (#245)
• FIX: Do not use deprecated --filter pandoc-citeproc generating boilerplate (e72eea5)
• FIX: Mask T1w images before transforming to template (#237)
• FIX: Account for label entity when querying brain mask (#257)
• MAINT: Run pytest on GitHub Actions (#262)
• MAINT: Mount TemplateFlow's home directory in CircleCI tests (#246)
• MAINT: Run black at the top level of the repo (#241)
• MAINT: Update to new API of NiWorkflows (#239)
• MAINT: Refactor Dockerfile and move tests from TravisCI to GHA (#240)
• MAINT: Use separate fallback cache for maint/0.7.x (#250)
• MAINT: CircleCI housekeeping (#258) (#259)

0.8.0rc2

A new minor release incorporating small iterations and improvements on
*NiWorkflows*, and including some bug-fixes/enhancements.

* FIX: Sturdier version check of sMRIPrep-wrapper package (#245)
* FIX: Do not use deprecated ``--filter pandoc-citeproc`` generating boilerplate (e72eea5)
* MAINT: Mount TemplateFlow's home directory in CircleCI tests (#246)
* MAINT: Run ``black`` at the top level of the repo (#241)
* MAINT: Update to new API of *NiWorkflows* (#239)
* MAINT: Refactor ``Dockerfile`` and move tests from TravisCI to GHA (#240)

0.8.0rc1

A new minor release incorporating small iterations and improvements on
*NiWorkflows*, and including some bug-fixes/enhancements.

  * FIX: Do not use deprecated ``--filter pandoc-citeproc`` generating boilerplate (e72eea5)
  * MAINT: Run ``black`` at the top level of the repo (#241)
  * MAINT: Update to new API of *NiWorkflows* (#239)
  * MAINT: Refactor ``Dockerfile`` and move tests from TravisCI to GHA (#240)

0.8.0rc0

A shim release pushing the pinning of *NiWorkflows* to allow the development
of *dMRIPrep* and *fMRIPrep* with the next 1.4.x series of *SDCFlows*.

0.7.1

Release Notes

Bug-fix release in the 0.7.x series.

All releases since 0.4.0 have incorrectly labelled T1w images normalized to a
template space as SkullStripped in the corresponding JSON sidecar files.
This affects 0.4.x through 0.4.2, 0.5.x through 0.5.3, 0.6.x through 0.6.2, and
0.7.0. Prior to 0.4.0, the images were actually skull-stripped, and the metadata
labels were not incorrect.

For backwards compatibility reasons, any future releases of these series will
have SkullStripped set to False. In 0.8 and above, the images will be skull-stripped
and the metadata set back to True.

CHANGES

• CI: CircleCI housekeeping (#234, #235)

0.7.0

Release Notes

Minor release in preparation for fMRIPrep 20.2.x LTS series.
Includes minor features and bug-fixes over the previous 0.6 series.

CHANGES

• FIX: Pin NiWorkflows 1.3.1 including bugfix for INU-correction failures (nipreps/niworkflows#567)
• FIX: Generate anatomical conversions with full spec from --output-spaces (#219)
• FIX: Ordering of probseg maps with anatomical fast-track (#214)
• FIX: Progress partial volume maps instead of posteriors (FSL FAST) (#213)
• ENH: Retain session info when multi-session data are not averaged (#225)
• ENH: Update derivatives description, .bidsignore for derivatives (#220)
• ENH: Add --no-tty option to Docker wrapper (#216)
• ENH: Add function to handle stale IsRunning files (#207)
• MAINT: Upgrade ANTs to 2.3.4 in Dockerfile (365673b)
• MAINT: Make workflows keyword-only (PEP 3102) (#208)

0.7.0rc2

Release Notes

Minor release in preparation for fMRIPrep 20.2.x LTS series.
Includes minor features and bug-fixes over the previous 0.6 series.

CHANGES

• FIX: Pin NiWorkflows 1.3.1 including bugfix for INU-correction failures (nipreps/niworkflows#567)
• FIX: Generate anatomical conversions with full spec from --output-spaces (#219)
• FIX: Ordering of probseg maps with anatomical fast-track (#214)
• FIX: Progress partial volume maps instead of posteriors (FSL FAST) (#213)
• ENH: Retain session info when multi-session data are not averaged (#225)
• ENH: Update derivatives description, .bidsignore for derivatives (#220)
• ENH: Add --no-tty option to Docker wrapper (#216)
• ENH: Add function to handle stale IsRunning files (#207)
• MAINT: Upgrade ANTs to 2.3.4 in Dockerfile (365673b)
• MAINT: Make workflows keyword-only (PEP 3102) (#208)

0.7.0rc1

Release Notes

Minor release in preparation for fMRIPrep 20.2.x LTS series.
Includes minor features and bug-fixes over the previous 0.6 series.

CHANGES

• FIX: Generate anatomical conversions with full spec from --output-spaces (#219)
• FIX: Ordering of probseg maps with anatomical fast-track (#214)
• FIX: Progress partial volume maps instead of posteriors (FSL FAST) (#213)
• ENH: Retain session info when multi-session data are not averaged (#225)
• ENH: Update derivatives description, .bidsignore for derivatives (#220)
• ENH: Add --no-tty option to Docker wrapper (#216)
• ENH: Add function to handle stale IsRunning files (#207)
• MAINT: Make workflows keyword-only (PEP 3102) (#208)

0.6.2

Release Notes

Bug-fix release addressing minor problems related to FreeSurfer handling.

CHANGES

• FIX: Adapt to the new FS canary interface (backwards compatible) (#205)
• FIX: Use t1w2fsnative_xfm to resample segmentations (#201)

0.5.3

Release Notes

Bug-fix release in the 0.5.x series.

This release fixes a bug where pre-run FreeSurfer that was not in alignment with the T1w template generated by fMRIPrep could result in misaligned segmentation and mask derivatives.

The bug is most likely to occur with pre-run FreeSurfer where multiple T1w images are found. It is easily evident in the first figure in the anatomical section of the reports, and will show heavily misaligned brain mask.

CHANGES

• FIX: Use t1w2fsnative_xfm to resample segmentations (#201)