From: Hoffmann, Malte,PhD <MHOFFMANN@mgh.harvard.edu>
Date: Monday, October 20, 2025 at 5:56 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>, Keith Jamison <kwj2001@med.cornell.edu>
Subject: Re: Applying synthmorph deformations using other tools

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You can convert a SynthMorph deformation field warp-sm.nii.gz to ITK/ANTs format using mri_warp_convert from a recent FreeSurfer release:

mri_warp_convert -g moving.nii.gz --inras warp-sm.nii.gz --outitk warp-itk.nii.gz

This warp can then be applied with ANTs tools, for example:

antsApplyTransforms -d 3 -i moving.nii.gz -r fixed.nii.gz -o moved.nii.gz -t warp-itk.nii.gz

________________________________________
From: Keith Jamison <kwj2001@med.cornell.edu>
Sent: Monday, October 20, 2025 18:07
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Applying synthmorph deformations using other tools

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I am trying to apply the synthmorph deformation fields using other tools so that I can combine multiple warps, use spline interpolation, etc. I have tried a few variations of the mri_convert and mri_warp_convert commands, but they either crash or result it skewed or otherwise incorrect outputs. Is there an example out there showing exactly what syntax I should use to convert a synthmorph deform.nii.gz output to something that can work with freesurfer mri_warp_convert, or with FSL or ANTs?

-Keith
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