Thank you for the above post @jdtournier
The following commands work fine for bringing tracts in MNI space:
sub=100307 cd /data/jet/dvp/HCP/$sub/mrtrix warp=/data/HCP_data/S900_2016_03_14/$sub/MNINonLinear/xfms/standard2acpc_dc.nii.gz warpconvert $warp -type displacement2deformation TCKwarp2MNI.nii.gz tcknormalise ComissL.tck TCKwarp2MNI.nii.gz ComissL_MNI.tck
For new users, note the selection of standard2acpc, which is counterintuitive, but this is what is needed to bring tracts in standard space.