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Dear Malte Thank you so much. I've tried both rigid and affine transformations, and I've attached a snapshot that shows how the CC doesn't fully overlap with the template. I'm using a high-quality DTI image and am wondering if incorporating a T1 image would help improve the registration. I'm not sure how to apply a two-step registration, if that's even possible, using mri_synthmorph. Thanks for your guidance.
Best, John
On Fri, Sep 1, 2023 at 1:27 PM Hoffmann, Malte,PhD < MHOFFMANN@mgh.harvard.edu> wrote:
External Email - Use CautionHi 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
External Email - Use CautionDear 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
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