Given ROIs fixedLabels.nii.gz, to be resampled into the space of movingImage.nii.gz, we would use the same warps:

${ANTSPATH}antsApplyTransforms \-d 3 \-i fixedImage.nii.gz \-r movingImage.nii.gz \
  -t [movingToFixed_0GenericAffine.mat, 1] \
  -t movingToFixed_1InverseWarp.nii.gz \-n GenericLabel-o fixedToMovingDeformed.nii.gz

but we add the option -n GenericLabel to specify interpolation that preserves label intensities

antsRegistrationSyN.sh -d 3 -n 20 -f bo.nii.gz -m MNI152_T1_1mm_brain.nii.gz -o regmni2t

antsApplyTransforms -d 3 -i mask.nii.gz -o testmask2template.nii.gz -r bo.nii.gz -t regmni2t1Warp.nii.gz -t regmni2t0GenericAffine.mat -n GenericLabel