I answered it yesterday. Check your inbox
On 11/16/2023 4:08 AM, Spapens, Jeltje (NP) wrote:
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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