Releases: nipreps/fmriprep
20.0.6
Release Notes
Bug-fix release in the 20.0.x series.
This release fixes a bug for phase-difference fieldmaps that are not in RAS+ orientation.
The bug presented as an error if the orientation was reordered relative to RAS+ (for example,
AIL+) and the swapped dimensions were not of the same size.
Otherwise, the bug introduced a poor masking of the phase difference map, and could be quite subtle
if the original orientation was LAS+.
Runs of fMRIPrep that used other susceptibility distortion correction (SDC) methods are not
currently considered problematic.
This bug affects all earlier versions of fMRIPrep, except for 1.5.10 and any future releases in
the 1.5.x series.
Changes
- FIX: Do not reorient magnitude images nipreps/sdcflows#98
1.5.10
effigies
Chris Markiewicz
Release Notes
Bug-fix release in the 1.5.x series.
This release fixes a bug for phase-difference fieldmaps that are not in RAS+ orientation.
The bug presented as an error if the orientation was reordered relative to RAS+ (for example,
AIL+) and the swapped dimensions were not of the same size.
Otherwise, the bug introduced a poor masking of the phase difference map, and could be quite subtle
if the original orientation was LAS+.
Runs of fMRIPrep that used other susceptibility distortion correction (SDC) methods are not
currently considered problematic.
This bug affects all previous versions of fMRIPrep, as well as versions 20.0.0-20.0.5.
Changes
- FIX: Do not reorient magnitude images (nipreps/sdcflows#98)
20.1.0rc1
Release Notes
The first release candidate of the fMRIPrep 20.1.x series. This release introduces a configuration
file to easily distinguish which options were selected for each participant, along with other enhancements.
Changes
- DOC: Add FAQ about reusing work directory (#2045)
- ENH: Config module (#2018)
- ENH: Add option to ignore T2w / FLAIR images (#2015)
- ENH: Ensure subcortical volume in CIFTI is in LAS orientation (nipreps/niworkflows#484)
- ENH: Add option to skip brain extraction (#2039)
- MAINT: Bump minimum Python to 3.7 (#2017)
20.0.5
Release Notes
Bug-fix release in 20.0.x series.
With thanks to James Kent for the fix and Blaise Frederick for the report and testing.
Changes
- FIX: Add CE agent to output figure filename templates (nipreps/niworkflows#482)
20.0.4
Release Notes
A bug-fix release improving documentation for filtering BIDS files and standardizing CIFTI volume orientation.
☘️🌈💰
With thanks to Ursula Tooley for the contribution.
Changes
- DOC: FAQ section for BIDS filter (#2028)
- FIX: Ensure BOLD and label orientations are equal (nipreps/niworkflows#477).
20.0.3
Release Notes
A bug-fix release for CIFTI surfaces.
This release remedies a resampling error when generating fsLR surfaces that was producing erroneous CIFTI files.
We strongly recommend all users who have generated CIFTI output with previous 20.0.x releases to upgrade and rerun.
Changes
- FIX: Remedy fsLR surface resampling (#2032)
20.0.2
Release Notes
A bug squashing release in the 20.0.x series.
This release fixes the use of custom templates within the docker wrapper, remedies crashes
when FreeSurfer HOME was not set, and improves the documentation for local installations.
With thanks to Blaise Frederick for the contribution.
Changes
20.0.1
Release Notes
Bug-fix release in 20.0.x series.
This release includes fixes for rare images with invalid qform matrices and some minor
improvements in report readability and inclusion of common templates in the Docker image.
CHANGES
- DOC: add --fs-subjects-dir usage to slurm example (#2003) @mgxd
- FIX: Handle qforms with invalid quaternions (nipreps/niworkflows#466) @effigies
- CI: Test that Docker image can run a common set of output spaces without network access (#1997) @effigies
- MAINT: Update niworkflows location (#2005) @mgxd
- ENH: Display errors as summary/details elements in reports (nipreps/niworkflows#464) @effigies
- ENH: Include low-res CIFTI templates in Docker image (#1996) @mgxd
20.0.0
Release Notes
The major release of 2020 is here!
fMRIPrep is transitioning to a calendar version system #1912.
The CalVer system reflects fMRIPrep's nature as an evolving workflow and does not impose any artificial incentive for "big-change" releases.
It also permits to quickly see how out-of-date someone's version is.
As of now, the default version increment is the minor release number.
Hence, when the minor release number changes the work directory of fMRIPrep will presumably break.
Micro releases only include bug-fixes that can reuse exiting working directories.
The major highlight of this release entails CIFTI generation to match HCP (Human Connectome Project) grayordinates.
In addition, the new fMRIPrep 20.0.0 has gone through a major overhaul in the handling of standard spaces (spatial normalizations, fusion of prior knowledge from corresponding atlases) and imaging outputs.
In particular, the new series almost completely implements the new syntax for --output-spaces to describe the (non)standard spatial references that shall be used for generating outputs #1604.
This release includes contributions from Azeez Adebimpe and Basile Pinsard - very much appreciated.
CHANGES
- ENH: Warn when existing output version does not match current pipeline version (#1967)
- ENH: Add
--clean-workdirargument (#1966) - ENH: Refactor of how spatial normalization targets and
--output-spacesare maintained (#1955) (#1983) - ENH: Add
--bids-filter-fileargument for more controlled data querying (#1770) - FIX: Ensure subject ID is used when selecting BIDS data (#1982)
- FIX: Display a log message when processing completes successfully (#1977)
- DOC: Clean up surface outputs (#1993)
- DOC: Integrate intersphinx, drop external module wrapping (#1989)
- DOC: Improve custom template usage description (#1969)
- MAINT: Use local docker registry (#1990)
- MAINT: Pin connectome-workbench 1.3.2, add to documented dependencies (#1958)
- MAINT: Pin NiBabel, NiWorkflows, sMRIPrep (#1971)
- MAINT: CI build error fixes (#1976)
