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 Caution
Hi 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" <dgr...@mgh.harvard.edu
<mailto:dgr...@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-b146-2b059dab1...@mgh.harvard.edu
<mailto:e31f2342-e539-4ecc-b146-2b059dab1...@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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