External Email - Use Caution
I have found the answer, thank you very much!
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@MGH.HARVARD.EDU Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, 16 November 2023 at 15.27 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem with brainstem overlap after BBR
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.spapens@maastrichtuniversity.nlmailto:j.spapens@maastrichtuniversity.nl Date: Wednesday, 8 November 2023 at 13.55 To: "Freesurfer@nmr.mgh.harvard.edu"mailto:Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edumailto: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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