Hi Josh,
Thank you for your interest in SynthMorph. FreeSurfer includes the tool
`mri_warp_convert` for converting between deformation field formats.
To convert to LPS displacements (ITK/ANTs format), you can use the following
command:
mri_warp_convert --inmgzwarp synthmorph.nii.gz --outitk ants.nii.gz
For FSL, there is a similar flag:
mri_warp_convert --inmgzwarp synthmorph.nii.gz --outfsl fsl.nii.gz
When you initialize the deformable registration with an affine transform, that
transform will be included in the output warp as is. However, joint
registration (and, similarly, initialized deformable registration with `-M`)
applies half the affine before and the other half after the deformation to
ensure end-to-end symmetry.
This means the warp lives in an affine mid-space that includes shear, and we're
currently exploring the best way to save it.
I hope this helps,
Malte
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Josh
<nimzodisas...@gmail.com>
Sent: Wednesday, December 11, 2024 18:50
To: Freesurfer support list
Subject: [Freesurfer] needed: tools to work with synthmorph deformations in
ANTS and FSL pipelines.
External Email - Use Caution
mri_synthmorph is simply an amazing SOTA tool that I want to incorporate into
all my pipelines. However, I am unsure how to convert the combined
affine+nonlinear deformation image into a format that can be worked with by
ants or FSL.
Optimally, synthmorph + lta_convert + mri_convert would provide tools to:
1. separate affine and nonlinear components of the registration (useful in
certain applications)
2. convert freesurfer transforms to current standard formats (FSL and ITK ants)
-Josh
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