Fmriprep

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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.

* FIX: Do not reorient magnitude images (`nipreps/sdcflows98`_)

.. _`nipreps/sdcflows98`: https://github.com/nipreps/sdcflows/pull/98

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Bug-fix release in 20.0.x series.

With thanks to James Kent for the fix and Blaise Frederick for the report and testing.

* FIX: Add CE agent to output figure filename templates (`nipreps/niworkflows482`_)

.. _`nipreps/niworkflows482`: https://github.com/nipreps/niworkflows/pull/482

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A bug-fix release improving documentation for filtering BIDS files and standardizing CIFTI volume orientation.

With thanks to Ursula Tooley for the contribution.

* DOC: FAQ section for BIDS filter (2028)
* FIX: Ensure BOLD and label orientations are equal (`nipreps/niworkflows477`_).

.. _`nipreps/niworkflows477`: https://github.com/nipreps/niworkflows/pull/477

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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**.

* FIX: Remedy fsLR surface resampling (2032)

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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.

* DOC: Update standalone installation requirements (2009)
* FIX: Crashes whenever FREESURFER_HOME is not set (2014)
* FIX: Local template mounting (wrapper) (2020)
* MAINT: Pin minor series of nipype, major series of nibabel (2021)

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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.

* FIX: Handle qforms with invalid quaternions (`nipreps/niworkflows466`_)
* FIX: update niworkflows location (2005)
* ENH: Display errors as summary/details elements in reports (`nipreps/niworkflows464`_)
* DOC: Add ``--fs-subjects-dir`` usage to slurm example (2003)
* CI: Test that Docker image can run a common set of output spaces without network access (1997)

.. _`nipreps/niworkflows464`: https://github.com/nipreps/niworkflows/pull/464
.. _`nipreps/niworkflows466`: https://github.com/nipreps/niworkflows/pull/466