Hi,
flirt -in myprefix0000.nii.gz -ref 5tt_nocoreg.nii.gz -interp nearestneighbour -dof 6 -omat diff2struct_fsl.mat
You should use the T1w to guide the registration, not the 5TT. It would be something like:
flirt -in myprefix0000.nii.gz -ref T1w.nii.gz -dof 6 -omat diff2struct_fsl.mat
transformconvert diff2struct_fsl.mat mean_b0_preprocessed.nii.gz T1w.nii.gz flirt_import diff2struct_mrtrix.txt
You can also play with other cost functions like bbr, please see here
And then, if your parcellation is already aligned with your T1w data, you only need to do:
mrtransform labels_nocoreg.mif -linear diff2struct_mrtrix.txt -inverse labels_coreg.mif
If is not, the first try to find the cause for this miss-alignment. The you have two options, or repeat the process with the other T1w, or align the two T1ws
Best regards,
Manuel