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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