Tags: effigies/fmriprep
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23.1.2 (June 16, 2023) Bug fix release in the 23.1.x series. This release correctly generates ``*_space-fsLR_desc-reg_sphere.surf.gii``, which was previously a copy of the standard ``*_desc-reg_sphere.surf.gii``. Additionally, warnings are now correctly emitted when AROMA-related CLI options are used. * CI: Clean up pre-release builds (nipreps#3040)
23.1.1 (June 14, 2023) Bug fix release in the 23.1.x series. This release corrects a small error that prevented the "goodvoxels" mask from being placed in the output directory if no FreeSurfer output spaces were specified. * FIX: Remove bad metadata input from ds_goodvoxels_mask (nipreps#3037)
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 nipreps#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 (nipreps#3028) * FIX: Inconsistent fmapless estimation when ignoring fieldmaps (nipreps#2994) * FIX: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2* map estimation (nipreps#2986) * FIX: Estimate free memory with "available", not "free" (nipreps#2985) * ENH: Add ``--me-t2s-fit-method`` parameter (nipreps#3030) * ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate (nipreps#3011) * ENH: Allow SBref+EPI PEPolar fieldmaps to correct BOLD series (nipreps#3008) * ENH: Remove ICA-AROMA from workflow and docs (nipreps#2966) * RF: Filter fieldmaps based on whether they will be used to correct a BOLD series (nipreps#3025) * MNT: Update ANTs pin in Docker image (nipreps#3016) * MNT: Update governance docs (nipreps#2992) * MNT: Refactor Docker build process (nipreps#2982) * MNT: Pin conda environment more strictly (nipreps#2853) * MNT: Require niworkflows ~1.3.6 (nipreps#2740) * CI: Use registry for layer caching (nipreps#3012) * CI: Upgrade docker orb (nipreps#2865)
23.1.0 (To be determined) 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 nipreps#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 (nipreps#3028) * FIX: Inconsistent fmapless estimation when ignoring fieldmaps (nipreps#2994) * FIX: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2* map estimation (nipreps#2986) * FIX: Estimate free memory with "available", not "free" (nipreps#2985) * ENH: Add ``--me-t2s-fit-method`` parameter (nipreps#3030) * ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate (nipreps#3011) * ENH: Allow SBref+EPI PEPolar fieldmaps to correct BOLD series (nipreps#3008) * ENH: Remove ICA-AROMA from workflow and docs (nipreps#2966) * RF: Filter fieldmaps based on whether they will be used to correct a BOLD series (nipreps#3025) * MNT: Update ANTs pin in Docker image (nipreps#3016) * MNT: Update governance docs (nipreps#2992) * MNT: Refactor Docker build process (nipreps#2982) * MNT: Pin conda environment more strictly (nipreps#2853) * MNT: Require niworkflows ~1.3.6 (nipreps#2740) * CI: Use registry for layer caching (nipreps#3012) * CI: Upgrade docker orb (nipreps#2865)
23.1.0rc0 (June 9, 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 nipreps#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 (nipreps#3028) * FIX: Inconsistent fmapless estimation when ignoring fieldmaps (nipreps#2994) * FIX: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2* map estimation (nipreps#2986) * FIX: Estimate free memory with "available", not "free" (nipreps#2985) * ENH: Add ``--me-t2s-fit-method`` parameter (nipreps#3030) * ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate (nipreps#3011) * ENH: Allow SBref+EPI PEPolar fieldmaps to correct BOLD series (nipreps#3008) * ENH: Remove ICA-AROMA from workflow and docs (nipreps#2966) * RF: Filter fieldmaps based on whether they will be used to correct a BOLD series (nipreps#3025) * MNT: Update ANTs pin in Docker image (nipreps#3016) * MNT: Update governance docs (nipreps#2992) * MNT: Refactor Docker build process (nipreps#2982) * MNT: Pin conda environment more strictly (nipreps#2853) * MNT: Require niworkflows ~1.3.6 (nipreps#2740) * CI: Use registry for layer caching (nipreps#3012) * CI: Upgrade docker orb (nipreps#2865)
23.0.1 (March 24, 2023) Bug fix release in the 23.0.x series. This release fixes issues with detecting partial fieldmaps, emitting a warning instead of an error. A small change in sMRIPrep fixes the name of a workflow, which may cause a duplication in a reused work directory from 23.0.0, but should not break any workflows or produce a change in derivatives.
23.0.0 (March 13, 2023) New feature release in the 23.0.x series. This release adds improvements for workflows targeting the fsLR grayordinate space. Namely, morphometric (curvature, sulcal depth and cortical thickness) measures are output as ``.dscalar.nii`` files and high-variance voxels can be excluded from the resampling step using ``--project-goodvoxels``. Additionally, T2w images are now resampled to the T1w-defined subject space if FreeSurfer reconstruction is used. If multiple T2w images are provided, they are merged into a single image first. PEPolar fieldmaps with R/L phase-encoding directions or in non-standard orientations are now better supported. We continue to work toward better support for more SDC configurations. 23.0.0 supports FreeSurfer 7.3.2, which is now bundled in the Docker image. ICA-AROMA support will be removed in 23.1.0. With thanks to Thomas Madison, Greg Conan, Celine Provins, Robert Smith and Yaroslav Halchenko for contributions. Thanks also to Steve Giavasis and colleagues at the Child Mind Institute for feedback on SDC processing. * FIX: Pass reference image to unwarp_wf, use reference fieldwarp for single shot (nipreps#2945) * FIX: Pass fmap filters to sdcflows (nipreps#2932) * ENH: Resample morphometrics to fsLR dscalar CIFTI-2 files if ``--cifti-output`` is used (nipreps#2959) * ENH: Add option to exclude projecting high variance voxels to surface (update of nipreps#2855) (nipreps#2956) * ENH: Separate deep from shallow WM+CSF in the carpetplot (nipreps#2744) * ENH: Merge T2w images and coregister to T1w template (nipreps#2941) * RF: Use DataFrame.rename instead of ad hoc process (nipreps#2937) * DOC: Update the description of the carpetplot in the sample report (nipreps#2950) * DOC: Altered CLI option grouping (nipreps#2944) * DOC: Update lesion ROI documentation, warn in docs and app about upcoming changes (nipreps#2943) * DOC: Update docs following read-through (nipreps#2930) * DOC: Update carpetplot in "Outputs of fMRIPrep" (nipreps#2923) * MNT: Codespell config, action + some typo fixups (nipreps#2958) * MNT: Warn that AROMA support will be removed in a future version (nipreps#2940) * MNT: Update Ubuntu, FreeSurfer, AFNI and Convert3D (nipreps#2931) * MNT: Switch to hatch build backend and update package metadata (nipreps#2914 + nipreps#2939) * MNT: Rotate CircleCI secrets and setup up org-level context (nipreps#2928) * CI: Minor updates to CircleCI config to improve resilience (nipreps#2957) * CI: Weekly docker build from scratch (nipreps#2938)
23.0.0rc0 (March 6, 2023) New feature release in the 23.0.x series. This release adds improvements for workflows targeting the fsLR grayordinate space. Namely, morphometric (curvature, sulcal depth and cortical thickness) measures are output as ``.dscalar.nii`` files and high-variance voxels can be excluded from the resampling step using ``--project-goodvoxels``. Additionally, T2w images are now resampled to the T1w-defined subject space if FreeSurfer reconstruction is used. If multiple T2w images are provided, they are merged into a single image first. 23.0.0 supports FreeSurfer 7.3.2, which is now bundled in the Docker image. ICA-AROMA support will be removed in 23.1.0. With thanks to Thomas Madison, Greg Conan, Celine Provins, Robert Smith and Yaroslav Halchenko for contributions. Thanks also to Steve Giavasis and colleagues at the Child Mind Institute for feedback on SDC processing. * FIX: Pass reference image to unwarp_wf, use reference fieldwarp for single shot (nipreps#2945) * FIX: Pass fmap filters to sdcflows (nipreps#2932) * ENH: Resample morphometrics to fsLR dscalar CIFTI-2 files if ``--cifti-output`` is used (nipreps#2959) * ENH: Add option to exclude projecting high variance voxels to surface (update of nipreps#2855) (nipreps#2956) * ENH: Separate deep from shallow WM+CSF in the carpetplot (nipreps#2744) * ENH: Merge T2w images and coregister to T1w template (nipreps#2941) * RF: Use DataFrame.rename instead of ad hoc process (nipreps#2937) * DOC: Update the description of the carpetplot in the sample report (nipreps#2950) * DOC: Altered CLI option grouping (nipreps#2944) * DOC: Update lesion ROI documentation, warn in docs and app about upcoming changes (nipreps#2943) * DOC: Update docs following read-through (nipreps#2930) * DOC: Update carpetplot in "Outputs of fMRIPrep" (nipreps#2923) * MNT: Codespell config, action + some typo fixups (nipreps#2958) * MNT: Warn that AROMA support will be removed in a future version (nipreps#2940) * MNT: Update Ubuntu, FreeSurfer, AFNI and Convert3D (nipreps#2931) * MNT: Switch to hatch build backend and update package metadata (nipreps#2914 + nipreps#2939) * MNT: Rotate CircleCI secrets and setup up org-level context (nipreps#2928) * CI: Minor updates to CircleCI config to improve resilience (nipreps#2957) * CI: Weekly docker build from scratch (nipreps#2938)
22.1.1 (January 04, 2023) Bug fix release in the 22.1.x series. This release fixes the reported version in the distributed Docker image, and depends on SDCFlows 2.2.2, which fixes a bug affecting SDC estimation in some oblique datasets. * FIX: Ensure version installed in Docker file is clean (nipreps#2922)
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