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