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.

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