22.0.2

Release Notes

A patch release in the 22.0.x series.

This release increases the minimum Nipype version to include better error messages on failures.
Additionally, this includes a fix to allow SyN distortion correction in combination with the
--ignore fieldmaps option.

Changes

• MAINT: Add pre-commit, dev installation for consistent styling (#2857)
• CI: Upgrade docker orb (#2858)

22.0.1

Release Notes

A patch release in the 22.0.x series.

This release includes relaxed tolerance in the case where fieldmap affines slightly differed,
and a fix for running FreeSurfer 7 with an outdated fsaverage folder.

Changes

• ENH: Add check to ensure latest fsaverage folder is used (#2847)
• FIX: Filter sbrefs by BIDS filters if available (#2843)
• FIX: Avoid crashing on empty ACompCor results (#2850)

22.0.0

Release Notes

New feature release in the 22.0.x series.

This release has been tested to work with Python 3.9 and FreeSurfer 7.2,
which are now bundled in the Docker image.

This release also features improvements to T2* and carpetplot reporting.

For the next release, we are investigating issues with susceptibility
distortion correction (SDC). Please check your results carefully and report
any issues you find.

Changes

• FIX: Update wrapper python path (#2783)
• FIX: Preserve collect_data behavior by using named args (#2754)
• FIX: Update fMRIPrep version in bibliography at run time (#2738)
• FIX: Plot carpetplot with CIFTI-specific colorbar (#2737)
• FIX: Two minor typos in report spec (#2708)
• ENH: Clip T2* values at 100ms to keep consistent histogram axes (#2781)
• ENH: Plot histogram of T2* values in gray-matter mask (#2778)
• ENH: Save T2starmap files in all requested output spaces, if calculated (#2776)
• ENH: Compare T2* map to BOLD reference (#2751)
• ENH: Add edge-regressors to confounds & crown to carpetplot (#2621)
• ENH: Add major/minor versions to base workflow name (#2716)
• DOC: Fix JSON typo in config in FAQ (#2771)
• DOC: Clarify calculation of confounding signals (#2724)
• MNT: Build on Python 3.9 environment (#2782)
• MNT: Seed ignore-revs file and script to tag new hashes with log entries (#2748)
• MNT: Require PyBIDS 0.15+ to allow fMRIPrep to preserve zero-padding in run entity (#2745)
• MNT: Upload artifacts after each step of Circle's workflow (#2736)
• MNT: Normalize code style of workflows.confounds (#2729)
• MNT: Ask for fmriprep-docker RUNNING line (#2670)
• DOCKER: Bundle FreeSurfer 7 (#2779)
• CI: Touch up CircleCI configuration (#2764)
• CI: Update package builds to use python -m build (#2746)

New Contributors

• @keithcallenberg made their first contribution in #2708
• @dillonplunkett made their first contribution in #2724
• @Remi-Gau made their first contribution in #2771

Full Changelog: 21.0.2...22.0.0

22.0.0rc4

This release candidate includes fixes for failing DVARS, running recon-all with T2w images, and misaligned GIFTI surfaces.

Full Changelog: 22.0.0rc3...22.0.0rc4

22.0.0rc3

This release candidate fixes an error that was encountered when filtering sessions with the --bids-filter-file.

22.0.0rc2

This release candidate includes missing FreeSurfer binaries that would result in recon-all sometimes failing.

22.0.0rc0

Release Notes

New feature release in the 22.0.x series.

This release has been tested to work with Python 3.9 and FreeSurfer 7.2,
which are now bundled in the Docker image.

This release also features improvements to T2* and carpetplot reporting.

Changes

• FIX: Update wrapper python path (#2783)
• FIX: Preserve collect_data behavior by using named args (#2754)
• FIX: Update fMRIPrep version in bibliography at run time (#2738)
• FIX: Plot carpetplot with CIFTI-specific colorbar (#2737)
• FIX: Two minor typos in report spec (#2708)
• ENH: Clip T2* values at 100ms to keep consistent histogram axes (#2781)
• ENH: Plot histogram of T2* values in gray-matter mask (#2778)
• ENH: Save T2starmap files in all requested output spaces, if calculated (#2776)
• ENH: Compare T2* map to BOLD reference (#2751)
• ENH: Add edge-regressors to confounds & crown to carpetplot (#2621)
• ENH: Add major/minor versions to base workflow name (#2716)
• DOC: Fix JSON typo in config in FAQ (#2771)
• DOC: Clarify calculation of confounding signals (#2724)
• MNT: Build on Python 3.9 environment (#2782)
• MNT: Seed ignore-revs file and script to tag new hashes with log entries (#2748)
• MNT: Require PyBIDS 0.15+ to allow fMRIPrep to preserve zero-padding in run entity (#2745)
• MNT: Upload artifacts after each step of Circle's workflow (#2736)
• MNT: Normalize code style of workflows.confounds (#2729)
• MNT: Ask for fmriprep-docker RUNNING line (#2670)
• DOCKER: Bundle FreeSurfer 7 (#2779)
• CI: Touch up CircleCI configuration (#2764)
• CI: Update package builds to use python -m build (#2746)

New Contributors

• @keithcallenberg made their first contribution in #2708
• @dillonplunkett made their first contribution in #2724
• @Remi-Gau made their first contribution in #2771

Full Changelog: 21.0.2...22.0.0rc0

21.0.2

Release Notes

This release includes a few bug-fixes for susceptibility distortion correction (SDC) and multi-echo (ME).
A few notable fixes include:

• Added tolerance for affine precision differences when using EPI fieldmaps.
• Removed hang-ups when reusing anatomical derivatives with ME data.
• Increased BOLD masking workflow robustness.

Changes

• DOCKER: Update multiarch deb package link (#2758)
• ENH: Add affine_tolerance flag to MergeSeries (nipreps/niworkflows#706)
• FIX: Initialize BIDS layout after cleaning working directory (#2741)
• FIX: Avoid double unwarping during resampling of processed multi-echo data (#2730)
• FIX: Account for potential lists of lists in multi-echo cases (nipreps/niworkflows#719)
• FIX: Improve reliability of BOLD masking workflow (nipreps/niworkflows#712)
• FIX: Relax tolerance for different affines when concatenating blips (nipreps/sdcflows#265)

21.0.1

Release Notes

Bug-fix release in the 21.0.x series.

This release re-enables reverse-PE EPI fieldmaps, i.e. EPIs acquired with the opposite phase-encoding direction to a BOLD series.
Additionally, the --use-syn-sdc option will now error by default if no PhaseEncodingDirection can be found for a BOLD series. To reduce this to a warning, use --use-syn-sdc warn. SyN-SDC will NOT be run, but the workflow will proceed.

NOTE:

topup runtime scales with the number of volumes used, so fMRIPrep defaults to using a maximum of 5 volumes from each of the BOLD series and the EPI fieldmap. To adjust this, please use the --topup-max-vols parameter.

Changes

• FIX: Create single fmap_select_std node for use with all ANAT estimators (#2692)
• FIX: Re-enable reverse-PE EPI fieldmaps (#2684)
• FIX: Pass boolean use_syn_sdc to find_estimators (#2685)
• FIX: Ensure AROMA inputs are uncompressed if --low-mem (#2657)
• ENH: Add --topup-max-vols flag to control TOPUP runtime (#2688)
• ENH: Allow --use-syn-sdc to take a "warn" option to avoid exiting when PE dir is unavailable (#2680)
• RF: Add extension field to differentiate from upcoming templates (#2613)
• WRAPPER: Map --bids-filter-file\s into Docker container (#2691)
• MNT: Silence warning from pybids; list packaging as dependency (#2689)
• MNT: Add netbase to Docker image to ensure correct datalad operation (#2682)
• MNT: Restore nitime to requirements, necessary for DVARS (#2678)

20.2.7 (Long-Term Support)

Release Notes

Bug-fix release in the 20.2.x LTS series.

Changes

• FIX: Clarify phase encoding direction, rather than axis (#2690)
• FIX: Ensure AROMA inputs are uncompressed if --low-mem (#2657)
• FIX: Add -basescale 1 parameter to avoid flirt scaling (#2624)
• WRAPPER: Map --bids-filter-file\s into Docker container (#2691)
• MNT: Add netbase to Docker image to ensure correct datalad operation (#2682)