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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:
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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


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