Registering CIT168-SubCorticalAtlas to Patient's QSM

Good Day,

I am new to Mrtrix and FSL. I am trying to register CIT168 Subcortical Mask to Patient’s QSM image. However, after I perform the command Mrgrid and Filrt , the mask seems out of position.

mrgrid CIT168_iAmyNuc_700um.nii.gz regrid -template Sepia_Chimap.nii.gz regrid_nucelus.nii -fill nan

flirt -in regrid_nucelus.nii -ref Sepia_Chimap.nii.gz -dof 12 -omat matrix_nucelus.mat -out filrt_nucelus.nii.gz

Previously, I have used the same method to register CIT168 Brain Mask to Patient’s QSM Image and was able to register brain mask properly on the QSM image.

mrgrid CIT168toMNI152-FSL_T1w_brain.nii.gz regrid -template Sepia_Chimap.nii.gz regrid_t1.nii -fill nan

flirt -in regrid_t1.nii -ref Sepia_Chimap.nii.gz -dof 12 -omat matrix.mat -out filrt.nii.gz

could someone with experience please advice ? was I suppose to use mrtransform ?