Is MRS_201_MT_tfl_stripped.mgz correctly oriented when you view it in
freeview? Also, bbr is meant to be used for within subject registration.
For something like registering to the mni152, try mri_coreg and specify
--dof 12
On 11/20/2023 10:00 AM, Spapens, Jeltje (NP) wrote:
External Email - Use Caution
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
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