[Freesurfer] Boundary based registration on partial FoV to MNI space

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Hello Freesurfer developers.

I tried the boundary-based registration of a partial FoV to a MNI space template with the following two step code:

bbregister --s MRS_201_recon_all --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_201/MRS_201_MT_tfl_stripped.mgz --reg MRS_201_NM2mp2rage.dat --t2 --init-header

mri_vol2vol --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_201/MRS_201_MT_tfl_stripped.mgz --targ /Users/robspapens/Desktop/Thesis/Subjects/MNI_upsamp.nii --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_201/MRS_201_MT_tfl_regt1.nii.gz --reg MRS_201_NM2mp2rage.dat --cubic

When I open the scan in Freeview or FSLeyes the orientation is not correct. The Horizontal plane is labeled as the Coronal plane and the sagittal plane is rotated 90 degrees.

I tried: fslreorient2std input_file.nii.gz output_file.nii.gz, but this gave the same result. I also tried it on 3 scans and all give the same wrong orientation after the BBR.

How can I best register the scan with small FoV to the MNI space template?

With kind regards,

Jeltje Spapens