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Thanks Malte!

Would you recommend anything between saving deform transforms generated from synthmorph, between .mgz or .nii.gz? Which in my case, are expected to be passed onto mri_warp_convert for itk conversion. I'm running numerous tests trying to find dissimilarities between the two approach, trying to determine which will be better for me.

Any insight?
De : freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Antoine Royer <Antoine.Royer@usherbrooke.ca>
Envoyé : 20 avril 2024 13:52
À : freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Objet : Re: [Freesurfer] Understanding registration with mri_synthmorph
 

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Thank you very much!!
De : freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Hoffmann, Malte,PhD <MHOFFMANN@mgh.harvard.edu>
Envoyé : 20 avril 2024 11:16
À : freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Objet : Re: [Freesurfer] Understanding registration with mri_synthmorph
 
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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Antoine Royer <Antoine.Royer@usherbrooke.ca>
Sent: Friday, April 19, 2024 16:08
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Understanding registration with mri_synthmorph

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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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