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You could try affine first and initialize the deformable registration with that. Something like:

mri_synthmorph -m affine fa.nii.gz template.nii.gz -t affine.txt mri_synthmorph -m deform -i affine.txt fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz

Alternatively, assuming your T1 is aligned with the FA map, you can run the above on the T1, save the warp with `-t warp.nii.gz` in the second call, and apply it to the FA map:

mri_warp_convert -g t1.nii.gz --inras warp.nii.gz --outm3z warp.m3z mri_convert -at warp.m3z fa.nii.gz fa_in_MNI.nii.gz

________________________________________ From: John Anderson jb19790001@gmail.com Sent: Friday, September 1, 2023 13:43 To: Freesurfer support list; Hoffmann, Malte,PhD Subject: Re: [Freesurfer] mri_synthmorph

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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.edumailto:MHOFFMANN@mgh.harvard.edu> wrote: External Email - Use Caution

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Anderson <jb19790001@gmail.commailto: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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