I have found the answer, thank you very much!

 

I answered it yesterday. Check your inbox

        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.spapens@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

 

 

 

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer