It looks like you are using MRS_200_UNI_MPRAGEised_stripped.nii for both the mov and the int. The int must be a full brain scan in registration with the slab. Also, it is better not to use --init-fsl (or any of the other --init-XXX flags)
On 1/4/2024 9:21 AM, Spapens, Jeltje (NP) wrote:
External Email - Use CautionHi Douglas,
I hope you had some nice holidays and a happy beginning of 2024.
Thank you for your suggestion. I have added the intermediate picture and changed the MRI_vol2vol target volume from the original scan to the MRI/T1 recon_all output. The latter one seemed to prevent the orientation shift. However, the registration still does not seem of very good quality. I have tried init-fsl, header and spm, but the first one gave the best results.
Do you have another advice for me?
bbregister --s MRS_200_recon_all --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.nii --t2 --int /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/presurf_MPRAGEise/MRS_200_UNI_MPRAGEised_stripped.nii --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat --init-fsl
mri_vol2vol --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.nii --targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_recon_all/mri/T1.mgz --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_regt1.nii.gz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat --cubic
Kind regards,
Jeltje Spapens
Message: 15 Date: Mon, 1 Jan 2024 16:07:00 -0500 From: "Douglas N. Greve" <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> Subject: Re: [Freesurfer] FW: Boundary based registration To:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <e31f2342-e539-4ecc-b146-2b059dab1b6c@mgh.harvard.edu mailto:e31f2342-e539-4ecc-b146-2b059dab1b6c@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8"
Have you tried using the "intermediate" option (--int) in bbregister? The intermediate volume should be a whole brain volume and it should share a RAS space with the slab volume (eg, if they were acquired in the same session; load both the slab and the intermediate in freeview to see if they are aligned). You can run bbregister with --help to get more info
On 12/13/2023 2:48 AM, Spapens, Jeltje (NP) wrote:
????????External Email - Use Caution
Hello Freesurfer developers,
I want to register an MRI slap to a full FoV UNI scan of the same subject, but I get a false reorientation with my code (see attached image). I have tried multiple input and tried the script on different subjects.
I also changed som flags such as -init-header and --cubic, but all seem to give the same results.
bbregister --s MRS_200_recon_all --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat --t2 --init-fsl
mri_vol2vol--mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz--targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_acpc_upsamp.nii --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_regt1.nii.gz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat ?trilin
I would appreciate to hear your thoughts on this problem.
Have a nice weekend and kind regards,
Jeltje Spapens
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