FIX: Set pixdim[4] to match RepetitionTime #679
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Hello @effigies, Thank you for updating! Cheers! There are no style issues detected in this Pull Request. 🍻 To test for issues locally, Comment last updated at 2022-03-09 17:25:17 UTC |
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@effigies ASL is similar to fmri (or bold) this will work |
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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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Via https://neurostars.org/t/modifying-nifti-files-before-fmriprep/21340/4, a dataset with
RepetitionTime == 2,pixdim[4] == 2000andxyzt_units & NIFTI_UNITS_MSEC == NIFTI_UNITS_MSEChas its outputs written out withRepetiionTime == 2,pixdim[4] == 2000andxyzt_units & NIFTI_UNITS_SEC == NIFTI_UNITS_SEC.This fix ensures that
RepetitionTimegets written topixdim[4]for BOLD series. This should avoid any conflicts with other 4+D data that doesn't have second units.@arokem @a3sha2 Are there any similar considerations for dMRI/ASL that we should fix while we're here?