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I have found the answer, thank you very much!
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve"
<dgr...@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:
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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><mailto:j.spap...@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.edu><mailto: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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