You are not going to be able to register the partial FoV directly to mni152. You can register the partial FoV to a full FoV within subject and then the full FoV to mni152, then concatenate the registrations together.
On 11/22/2023 8:01 AM, Spapens, Jeltje (NP) wrote:
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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 <https://secure-web.cisco.com/1ErgZtqa9Yd4vO6RXJFeU2F9cIPUxOgpmslxgpM84PAZUxIaPsHfUfI1WyItYXAuRWUUPhu9FkyC81FE3OuOxjRRwOUFT3KwvllusnWLA1DJjpIaqqW3Tp3BvmFrqIB6ruOQRGK2ftuGSkkdM9kEEETosjGmqpjy9Jr3XNNZcWvrK6us8iUzIhZxh0RZN8ozpFETU_4GZnThE3yAhvjPaFVKqrT_kYs5JuTuAy6VHhY45saSnnFB6oi84e4vrxLapGiYxU-LXIeH3hjgyDUTl-57LFEBoFR91ql6GIhsRyqsG2TuxJcqq-Lk5GG5PANpSUb1a9oVraT8skVEqiXfqzA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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