External Email - Use Caution Hello Freesurfer Developers,
I have never received an answer to my problem, maybe it was lost in the e-mails. Kind regards, Jeltje Spapens From: "Spapens, Jeltje (NP)" <j.spap...@maastrichtuniversity.nl> Date: Wednesday, 8 November 2023 at 13.55 To: "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu> Subject: Problem with brainstem overlap after BBR Hello Freesurfer Developers, I have performed a boundary-based registration followed by a mri_vol2vol on a Neuromelanin sensitive MRI scan (partial FoV) with a T1 structural scan. I used this code: Boundary-based registration in Freesurfer Set the environment in the terminal. bbregister --s MRS_203_recon_all --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_stripped.mgz --reg MRS_203_NM2mp2rage.dat --T1 --init-fsl mri_vol2vol --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_stripped.mgz --targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_upsamp.nii --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_regt1.nii.gz --reg MRS_203_NM2mp2rage.dat –cubic I performed the analysis on two participants, but the brainstem does not overlap very nicely. I attached the screenshots of Freeview of the two participants with the T1 scan and the NM scan after the BBR. Our analysis focuses on the Substantia Nigra. I also attached the full script that we use including the pre analysis. Do you have a tip how to improve the BBR to reach better overlap. Kind regards, Jeltje Spapens
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