External Email - Use Caution Hi I have not received a response to my question yet I think __
On 13/12/2023, 08.53, "freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of freesurfer-requ...@nmr.mgh.harvard.edu <mailto:freesurfer-requ...@nmr.mgh.harvard.edu>" <freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of freesurfer-requ...@nmr.mgh.harvard.edu <mailto:freesurfer-requ...@nmr.mgh.harvard.edu>> wrote: Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/13w96AyqB5Nk5Zlu_uq8_qAk6WErZ9a6rflAusUqF0Icp2MEBV8MM3a7HRD9qgxdTmVdygA79a8TVer1oIvAisAwiZwSn4GamqCNH78hF6y866lKZTazVDZUkb-1RNJ-mIPo13tA3o8h9xg0P6w7oa3p1ehEYBCMOlxPf5PMNbYzXUv_wFgREmuSlqTXSZkMnUN0l0U0b583YkxrNeH2rct82mhybDb-FxXyyGLc51JToYuCFGcO81tTjWZA8abucBn9XOL8SlBUZO-mlM5VJfwOy8wHX_-X4NyC3jTfiSF1uAQjF3Q65GKvQQI-KCnDS/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/13w96AyqB5Nk5Zlu_uq8_qAk6WErZ9a6rflAusUqF0Icp2MEBV8MM3a7HRD9qgxdTmVdygA79a8TVer1oIvAisAwiZwSn4GamqCNH78hF6y866lKZTazVDZUkb-1RNJ-mIPo13tA3o8h9xg0P6w7oa3p1ehEYBCMOlxPf5PMNbYzXUv_wFgREmuSlqTXSZkMnUN0l0U0b583YkxrNeH2rct82mhybDb-FxXyyGLc51JToYuCFGcO81tTjWZA8abucBn9XOL8SlBUZO-mlM5VJfwOy8wHX_-X4NyC3jTfiSF1uAQjF3Q65GKvQQI-KCnDS/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu <mailto:freesurfer-ow...@nmr.mgh.harvard.edu> When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. FW: Boundary based registration (Spapens, Jeltje (NP)) ---------------------------------------------------------------------- Message: 1 Date: Wed, 13 Dec 2023 07:48:55 +0000 From: "Spapens, Jeltje (NP)" <j.spap...@maastrichtuniversity.nl <mailto:j.spap...@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-1b1486646...@maastrichtuniversity.nl <mailto:802b8ce8-cf05-4066-809e-1b1486646...@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 -------------- next part -------------- An HTML attachment was scrubbed... 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