Have you tried using the "intermediate" option (--int) in bbregister? The intermediate volume should be a whole brain volume and it should share a RAS space with the slab volume (eg, if they were acquired in the same session; load both the slab and the intermediate in freeview to see if they are aligned).
You can run bbregister with --help to get more info

On 12/13/2023 2:48 AM, Spapens, Jeltje (NP) wrote:

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Hello Freesurfer developers,

I want to register an MRI slap to a full FoV UNI scan of the same subject, but I get a false reorientation with my code (see attached image). I have tried multiple input and tried the script on different subjects.

I also changed som flags such as -init-header and --cubic, but all seem to give the same results.

bbregister --s MRS_200_recon_all --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat --t2 --init-fsl

mri_vol2vol --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz --targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_acpc_upsamp.nii --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_regt1.nii.gz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat –trilin

I would appreciate to hear your thoughts on this problem.

Have a nice weekend and kind regards,

Jeltje Spapens
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