Hi Douglas,

Thank you for your feedback. I registered the anatomical T1 scan (output recon-all) to the MNI image with FLIRT (MRS_101_FLIRT.nii). So, I decided to register the partial FoV scan (MRS_101_MT_tfl_stripped.nii) to the MRS_101_FLIRT.nii.

I tried both bbregister and mricoreg, but both did not work. The bbregister output had an oblique output and was registered to the wrong image. The mri_coreg did not correctly register as seen in the screenshot.

I used following commands:

bbregister

bbregister --s MRS_101_recon_all --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_MT_tfl_stripped.nii --reg MRS_101_NM2mp2rage.dat --t2 --init-header

mri_vol2vol --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_MT_tfl_stripped.nii --targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_FLIRT.nii --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_MT_tfl_regt1.nii.gz --reg MRS_101_NM2mp2rage.dat –cubic

mri_coreg

mri_coreg --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_MT_tfl_stripped.mgz --targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_FLIRT.nii --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_coregistration.lta

mri_vol2vol --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_MT_tfl_stripped.mgz --targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_FLIRT.nii --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_coregistration.lta --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_coregistered.mgz

Kind regards,

Jeltje Spapens

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: Tuesday, 21 November 2023 at 18.31
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Boundary based registration on partial FoV to MNI space

Is MRS_201_MT_tfl_stripped.mgz correctly oriented when you view it in freeview? Also, bbr is meant to be used for within subject registration. For something like registering to the mni152, try mri_coreg and specify --dof 12

On 11/20/2023 10:00 AM, Spapens, Jeltje (NP) wrote:

External Email - Use Caution

Hello Freesurfer developers.

I tried the boundary-based registration of a partial FoV to a MNI space template with the following two step code:

bbregister --s MRS_201_recon_all --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_201/MRS_201_MT_tfl_stripped.mgz --reg MRS_201_NM2mp2rage.dat --t2 --init-header

mri_vol2vol --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_201/MRS_201_MT_tfl_stripped.mgz --targ /Users/robspapens/Desktop/Thesis/Subjects/MNI_upsamp.nii --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_201/MRS_201_MT_tfl_regt1.nii.gz --reg MRS_201_NM2mp2rage.dat --cubic

When I open the scan in Freeview or FSLeyes the orientation is not correct. The Horizontal plane is labeled as the Coronal plane and the sagittal plane is rotated 90 degrees.

I tried: fslreorient2std input_file.nii.gz output_file.nii.gz, but this gave the same result. I also tried it on 3 scans and all give the same wrong orientation after the BBR.

How can I best register the scan with small FoV to the MNI space template?

With 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