Hi Antoine,
Thanks for reaching out. Unless you're using a dev build of FreeSurfer,
mri_synthmorph may lag behind the dockerized version, which is likely why you
see a different behavior. For affine transforms, we switched to LTA format to
track the source and target spaces. SynthMorph now saves these with surfa,
which insists on the .lta suffix.
Similarly, we recently added code to save warp files in .mgz format, which is
more similar to NIfTI and less clunky than .m3z (surfa might not let you save
warps with NIfTI extension just yet). Until the next FS release, I would
recommend using SynthMorph from the Docker Hub.
In any case, the warps store shifts in physical RAS space: your
`mri_warp_convert` call looks correct, and `antsApplyTransforms -v -d 3 -i
[moving] -r [fixed] -t ants_warp.nii.gz -o out.nii.gz` should produce an image
identical to "warped.nii.gz".
Malte
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Antoine Royer
<antoine.ro...@usherbrooke.ca>
Sent: Friday, April 19, 2024 16:08
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Understanding registration with mri_synthmorph
External Email - Use Caution
Hi all!
I am working on implementing some freesurfer synth tools into a larger
diffusion processing pipeline. Doing so, I would like to use mri_synthmorph to
generate a transform and then pass it downstream. FIrstly, I use the dockerized
synthmorph version, which seems to present discrepancies in its behaviour vs
local testing:
1.
Can someone explain the expected output format of freesurfer transforms? When
used within docker, I must define affine transforms as .lta and deform
transforms as .mgz, otherwise: "ValueError: cannot determine file format from
extension for test__init_warp.txt"; while when using mri_synthform from my
local freesurfer installation, it doesn't seem like an issue. While I expected
.m3z to be the expected output.
2.
Here is the sequence of functions I use. My objective is to pass down the
resulting transform (affine initialization + deform warp) downstream my
pipeline for further registration using ANTs (antsApplyTransforms). I tested
and it seems to work, but i would appreciate an opinion. Does the --insrcgeom
parameter fixes everything for me?
*
Initialization + registration (freesurfer):
*
mri_synthmorph -m affine -t <init.lta> [moving] [fixed]
mri_synthmorph -m deform -t <freesurfer_warp.mgz> -o <warped.nii.gz> -i
<init.txt> [moving] [fixed]
Convert warp from freesurfer (RAS) to ANTs (LPS) using freesurfer warp_convert:
mri_warp_convert -g [moving] --inras <freesurfer_warp.mgz> --outlps
<ants_warp.nii.gz>
Thank you very much!
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