External Email - Use Caution

Hi I have not received a response to my question yet I think __

On 13/12/2023, 08.53, "freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:

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Today's Topics:

1. FW: Boundary based registration (Spapens, Jeltje (NP))

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Message: 1 Date: Wed, 13 Dec 2023 07:48:55 +0000 From: "Spapens, Jeltje (NP)" <j.spapens@maastrichtuniversity.nl mailto:j.spapens@maastrichtuniversity.nl> Subject: [Freesurfer] FW: Boundary based registration To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <802B8CE8-CF05-4066-809E-1B14866460CB@maastrichtuniversity.nl mailto:802B8CE8-CF05-4066-809E-1B14866460CB@maastrichtuniversity.nl> Content-Type: text/plain; charset="utf-8"

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