External Email - Use Caution 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 ? On Wed, Dec 11, 2024 at 3:50 PM Josh <nimzodisas...@gmail.com> wrote: > 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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