Proper codes and steps for Registration

I have encountered some difficulty in trying to align standard masks to the native space. My advisor and I just decided to feed the inverted affine matrix into probtrackx2 with the code:

flirt -in nodif_brain_mask (B0) -ref /packages/7x/fsl/6.0.2/data/standard/MNI152_T1_2mm_brain -out diff2struct_reg -omat mask2struct.mat

convert_xfm -omat mask2struct -inverse inv_mask2struct_01.mat

I resmapled the ROIs and binarized, for example:

flirt -in medialtempL.nii.gz -ref fits_FA.nii.gz -applyisoxfm 2.0 -out medialtempL_reg.nii.gz

fslmaths medialtempL_reg.nii.gz -thr 0.5 -bin resmedialtempL.nii.gz

Yet, when I ran the tractography, the results were still not aligned properly. This is creating an issue for my thresholding of the streamlines . This is the probtrackx2 command:

probtrackx2 -s ./merged -m bw_nodif_brain_mask.nii.gz --seed=resSN_seed.nii.gz --xfm=mask2struct.mat --xfm=inv_mask2struct_01.mat --out=fdt_paths --opd --targetmasks=/home/jeterry3/DTI_Images/PD_029/AxialDTI64Dir_801/seeds_to_targets_00.txt --stop=/home/jeterry3/DTI_Images/PD_029/AxialDTI64Dir_801/seeds_to_targets_00.txt --os2t --s2tastext -P 5000 -S 2000 --steplength=0.5 -c 0.2

So, I went back and tried to make changes.

I registered the B0 to the FA ( I don’t have a T1)
I registered the output of that to the MNI152_T1_2mm_brain

But when I tried to do the fnirt with the unbetted data, the transform came out as a big grey pixelated square.

What is going wrong with FNIRT and with the Probtrackx2 ( transformation matrix)?