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:
External Email - Use Caution
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-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: *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
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