Releases: nipreps/fmriprep
20.1.0rc3
*fMRIPrep* 20.1.0 introduces a magnitude of new features and improvements.
Originally nominated to become the first LTS (long-term support) version of *fMRIPrep*, this release has been supercharged with many new features and bug-fixes.
To ensure long-term stability, we have postponed the LTS nomination to 20.2 to allow us unlocking the 20.1 earlier, and a more extensive stress testing of the series before jumping into a longer support commitment.
Some key additions in this release include:
- A centralized `configuration module
<https://fmriprep.readthedocs.io/en/latest/api.html#module-fmriprep.config>`__
keeping track of *fMRIPrep*'s many options and run-time and environmental
circumstances and settings.
The new config module, which has been also propagated to other *NiPreps*
(`dMRIPrep <https://nipreps.org/dmriprep>`__,
`MRIQC <https://mriqc.readthedocs.io/>`__),
comes to robustify the run-to-run replicability of *fMRIPrep* (e.g., tracking random seeds),
make the option handling more modular but consistent (e.g., setting the ground for a
command-line interface built off of the config module),
and ease troubleshooting and telemetry.
- The *anatomical preprocessing fast-track*: a new command-line option
``--anat-derivatives <PATH>`` checks that all necessary anatomical derivatives
required by *fMRIPrep* are present under ``<PATH>``, and skips the anatomical
processing in full if *fMRIPrep*'s expectations are met.
Because now functional processing of many sessions and runs can be efficiently
split into more digestible computational units (i.e., cluster job) while guaranteeing the
exact same anatomical results are being used, this can significantly speed up
longitudinal study preprocessing, and it is a fundamental optimization to process
databases of densely scanned individuals such as `My Connectome
<https://openneuro.org/datasets/ds000031>`__.
- A change in output CIFTI2 subcortical volume orientation to be compatible with HCP Pipeline tools and data.
.. admonition:: Thanks
With thanks to Basile Pinsard, Joe B. Wexler, Noah Benson, and Marc Bue for contributions.
.. admonition:: New Paper!
This release comes after our latest protocol paper "*Analysis of task-based
functional MRI data preprocessed with fMRIPrep*" has been accepted.
The protocol describes how to use *fMRIPrep* on high-performance
clusters to preprocess fMRI data for task-based analyses.
Please check out `the latest version on Nature Protocols
<https://doi.org/10.1038/s41596-020-0327-3>`__ or `the preprint
<https://doi.org/10.1101/694364>`__.
.. caution::
As with all minor version increments, working directories
from previous versions **should not be reused**.
Thank you for using *fMRIPrep*!
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.
* FIX: Temporary config file in work directory gets clobbered in parallel jobs (#2138)
* FIX: Dismiss ``echo`` entity on several derivatives and figures outputs (#2133)
* FIX: Correct summary report when using previously run ``recon-all`` (#2124)
* FIX: Ensure correct WM and CSF masks are picked in confounds workflow (#2128)
* FIX: Explicitly add default ``native`` resolution to volumetric outputs (`nipreps/niworkflows#494`_)
* ENH: Finish the upstreaming of *NiTransforms* interfaces to *NiWorkflows* (#2132)
* ENH: Enable filtering for ``ANY`` or ``NONE`` in ``--bids-filter-file`` (#2123)
* ENH: Use new ``DerivativesDataSink`` from *NiWorkflows* 1.2.0 (#2114)
* 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)
* ENH: Use CIFTI sampling for carpetplot when available (#2055)
* MAINT: Stop printing full boilerplate, ``black fmriprep/cli`` (#2119)
* MAINT: Ensure YAML loader is specified (#2125)
* MAINT: PIN *tedana* version (#2117)
* MAINT: Bump minimum Python to 3.7 (#2017)
* MAINT: Remove unused console scripts (#2048)
* MAINT: Reduce the overall size of outputs (`nipreps/niworkflows#492`_)
* DOC: Update parallel subject neurostars link in FAQ (#2104)
* DOC: Add FAQ about reusing work directory (#2045)
.. _`nipreps/niworkflows#484`: https://github.com/nipreps/niworkflows/pull/484
.. _`nipreps/niworkflows#494`: https://github.com/nipreps/niworkflows/pull/494
.. _`nipreps/niworkflows#492`: https://github.com/nipreps/niworkflows/pull/492
20.0.7
Release Notes
Bug-fix release in the 20.0.x series.
Changes
This release includes a new, portable version of the templateflow python client. This features an automatic check to fetch the most recent templateflow templates every time.
- MAINT: Bump templateflow to auto-update template skeleton
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
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