Warping any priors in atlas space to subject space 😉

-- Juan Eugenio Iglesias http://www.jeiglesias.com From: Maurilio Genovese mauriliogenovese@gmail.com Date: Tuesday, May 12, 2026 at 1:42 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Move mri_super_synth output in MNI space

External Email - Use Caution Thank you for your answer. As I can see, the output files are already in the subject space (except for 1x1x1 resampling). Which is the purpose of the mni to subject warp included in the output folder? Is it just a substep of the analysis?

Maurilio

Il mar 12 mag 2026, 19:12 Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> ha scritto: 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.comhttp://secure-web.cisco.com/1jz9ES4xdbdGk2QEikXmEC4kM2NkUg2MvRl7-dO5hwdRwUt2sVwb72WKgHs60NA4ko8pSqrqnctGyVK9RGG5fHd7ZD72vSmXoiq68HizosreioshfvpIdzrqw1cEBfAVtY9t1a41XZV5J6m_llEcJezqi6nnT9hSg_mYrMet38EG-oIIRgQW7ItXtHHT-VIIZqYNioGtG8ExzBnvzqhrQRc7wcF2Ll8fuqhVTkmxxEbZbLY3G1F9VjIsulmsHoEuei7OyQEWRN541Eoel9P_Vyj9Dil2UfbtXBQWGoP-9mUUDmCJaFk17VYixmYrve5HH/http%3A%2F%2Fwww.jeiglesias.com From: Maurilio Genovese <mauriliogenovese@gmail.commailto:mauriliogenovese@gmail.com> Date: Tuesday, May 12, 2026 at 2:03 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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

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