For some reason the replies I see on the mail archive are not showing up in my mail server.
I am using synthmorph from its latest docker freesurfer/synthmorph:latest and am trying to use the mri_convert_warp from docker image freesurfer/freesurfer:7.4.1, with this command:
mri_warp_convert --inmgzwarp 106682-100.nii_to_template_final_deform.nii.gz --outitk test.nii.gz
and I get ERROR: Option: --INMGZWARP unknown (see --help) !!
Is this option newer than 7.4.1?
Also synthmorph documentation says deformation are in RAS space, so mri_warp_convert --inras warp.nii.gz --outitk warp.nii.gz ?
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