External Email - Use Caution
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
Several things - don't use --init-fsl. If you don't specify, then it will use mri_coreg, which will work better. You can also try --init-header - your movable scan appears to be t2 weighted, so use --t2 instead of --t1 - look at the cost file (or send it). It is hard to say what the cost should be, but my guess from your data is that it should be below 0.5 - when you send pics, load the surfaces as that makes it really easy to tell whether the registration is good or not - where these data sets acquired in the same session? If not, or if the subject moved a lot, then you might have to include an intermediate volume
On 11/8/2023 7:55 AM, Spapens, Jeltje (NP) wrote:
External Email - Use Caution
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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.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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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Douglas N. Greve -
Spapens, Jeltje (NP)