FIX: Set pixdim[4] (repetition time) in seconds #2740
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effigies
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Jun 12, 2023
23.1.0 (June 12, 2023) New feature release in the 23.1.x series. This release substantially reworks the resampling to fsLR grayordinate space, better accounting for partial volumes and high variance voxels. If you are resampling using ``--project-goodvoxels``, we strongly recommend upgrading. Fieldmap handling is improved, with better preference given to single-band references in both PEPolar and SyN-SDC schemes. Additionally, fMRIPrep will no longer estimate fieldmaps that are not intended to be used to correct BOLD series, reducing unneeded processing. This release removes ICA-AROMA from the fMRIPrep workflow. To use ICA-AROMA, set ``MNI152NLin6Asym:res-2`` as a target output space. MELODIC and ICA-AROMA can be run on the resulting images in a separate pipeline. For further information on the reasoning behind this change, see `GitHub issue #2936 <https://github.com/nipreps/fmriprep/issues/2936>`__. This release increments the versions of ANTs and FSL bundled in the Docker image. With thanks to Eilidh MacNicol, Basille Pinsard and Taylor Salo for contributions in fMRIPrep and SDCflows. * FIX: Raise RuntimeError at build if echos have mismatched shapes (#3028) * FIX: Inconsistent fmapless estimation when ignoring fieldmaps (#2994) * FIX: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2* map estimation (#2986) * FIX: Estimate free memory with "available", not "free" (#2985) * ENH: Add ``--me-t2s-fit-method`` parameter (#3030) * ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate (#3011) * ENH: Allow SBref+EPI PEPolar fieldmaps to correct BOLD series (#3008) * ENH: Remove ICA-AROMA from workflow and docs (#2966) * RF: Filter fieldmaps based on whether they will be used to correct a BOLD series (#3025) * MNT: Update ANTs pin in Docker image (#3016) * MNT: Update governance docs (#2992) * MNT: Refactor Docker build process (#2982) * MNT: Pin conda environment more strictly (#2853) * MNT: Require niworkflows ~1.3.6 (#2740) * CI: Use registry for layer caching (#3012) * CI: Upgrade docker orb (#2865)
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Jul 18, 2024
20.2.8 (July 18, 2024) Bug-fix release in the 20.2.x LTS series. We anticipate this being the final release in the 20.2.x LTS series. * FIX: Select volumetric dseg.tsv from recent TemplateFlow releases (#3257) * FIX: LTS package build (#3328) * DOC: Read html_baseurl from RTD environment, if available (#3324) * DOCKER: Pin conda environment more strictly (#2853) * MNT: Require niworkflows ~1.3.6 (#2740) * CI: Upgrade docker orb (#2865) This release includes a number of fixes that have accumulated in niworkflows, including the following fixes that affect fMRIPrep: * FIX: Remove unused ANTs parameter that was removed in 2.4.1 (nipreps/sdcflows#431) * FIX: Limit 3dQwarp to maximum 4 CPUs for stability reasons (nipreps/sdcflows#128) * MAINT: Make call to scipy.stats.mode compatible with scipy 1.11.0 (nipreps/sdcflows#371) * FIX: TSV2JSON should convert empty TSV files to empty JSON files (nipreps/niworkflows#747) * FIX: Use copy function that does not preserve mtime when creating fsaverage directories (nipreps/niworkflows#703) * FIX: Set pixdim[4] to match RepetitionTime (nipreps/niworkflows#679)
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In cases when the input BOLD series has
pixdim[4]in ms, we update the output series to have the temporal units of seconds, but do not set thepixdim[4]field to seconds. This release of niworkflows fixes that.Low priority for release, IMO.