External Email - Use Caution
It worked, thanks!
I used --outvox instead if --outfsl, as --outfsl was "not implemented yet" (using dev) and it feels safer since the m3z seems to have voxel units.
For posterity, below is a snippet of the code I used:
gradFile=/space/freesurfer/unwarp/gradient_nonlin_unwarp/gradient_coil_files/coeff_SC72CD.grad for epiFile in $curBidsDir/func/*_bold.nii.gz; do curDerivDir=$(basename $epiFile) curDerivDir=${curDerivDir%.nii.gz} curDerivDir=$derivDir/${curDerivDir%.nii.gz} mkdir -p $curDerivDir ln $epiFile $curDerivDir/epi.nii.gz ### Compute warp mri_gradunwarp --gradcoeff $gradFile \ --i $curDerivDir/epi.nii.gz \ --interp cubic \ --o $curDerivDir/gradCor_epi.nii.gz \ --out_transtbl $curDerivDir/epi_gradWarp.m3z \ --nthreads 10 ### Zero-out z mri_warp_convert \ --inm3z $curDerivDir/epi_gradWarp.m3z \ --outvox $curDerivDir/epi_gradWarpVOX.nii.gz mri_convert -i $curDerivDir/epi_gradWarpVOX.nii.gz --split -o $curDerivDir/epi_gradWarpVOX.nii.gz mri_binarize --i $curDerivDir/epi_gradWarpVOX0002.nii.gz \ --min -inf --max +inf --binval 0 \ --o $curDerivDir/epi_gradWarpVOX0002.nii.gz mri_concat --o $curDerivDir/epi_gradWarpVOX.nii.gz --i $curDerivDir/epi_gradWarpVOX000?.nii.gz mri_warp_convert \ --invox $curDerivDir/epi_gradWarpVOX.nii.gz \ --insrcgeom $curDerivDir/epi.nii.gz \ --outm3z $curDerivDir/epi_gradWarpNoZ.m3z ### Clean rm $curDerivDir/epi_gradWarpVOX*nii.gz done