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Hi John,
Currently, the default transformation model is "deform". Could you check if "affine" yields a better result?
mri_synthmorph -m affine fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz
Cheers, Malte
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of John Anderson jb19790001@gmail.com Sent: Friday, September 1, 2023 12:45 To: Freesurfer support list Subject: [Freesurfer] mri_synthmorph
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Dear Freesurfer experts, I processed DTI data using dt_recon, and I want to register FA images to the standard MNI152 space. However, after running the command mri_synthmorph fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz,
the registration is not accurate. I'm not sure what I've done wrong. Thank you for any guidance.
sincerely J