Dear Maurilio

The transform goes from MNI to subject space, and is not easily invertible (well, the affine part is!).

You can apply linear transforms with eg mri_convert as:

mri_convert moving.mgz output.mgz -rl reference.mgz -at linear_transform.lta

Or, -ait instead of -at to apply the inverse (linear) transform.

Cheers,

/Eugenio

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: Maurilio Genovese <mauriliogenovese@gmail.com>
Date: Tuesday, May 12, 2026 at 2:03 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Move mri_super_synth output in MNI space

External Email - Use Caution

Hi FreeSurfer Experts,
I have successfully run mri_super_synth and obtained the following outputs: mni_deformation.mgz, mni_affine.txt, and segmentation.mgz.

I am now trying to warp the segmentation to MNI space. I converted the .txt affine matrix to .lta format, but when I run mri_vol2vol, the output is not in the correct mni space:

mri_vol2vol --mov ribbon.mgz \
--targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz \
--m3z /path/to/mni_deformation.mgz \
--lta ./mni_affine.lta \
--o seg_mni.nii.gz \
--interp trilinear \
--noDefM3zPath

Thanks,

Maurilio Genovese