Hi Peter,
Here is an example to convert from native space to MNI305 (fsaverage) in
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2vol
mri_vol2vol --mov orig.mgz
--targ $FREESURFER_HOME/average/mni305.cor.mgz
--xfm transforms/talairach.xfm
--o orig-in-mni305.mgz
In your case, I think you also need ‘—interp nearest’ to convert segmentation.
To convert from fsaverage to native space of a subject, can you try the
following? I used bert as an example.
mri_vol2vol
--mov bert/mri/orig.mgz
--targ fsaverage/mri/aseg.mgz
--xfm transforms/talairach.xfm
--inv
--o aseg-from-mni305.mgz
--interp nearest
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of P Pieperhoff
Sent: Thursday, November 16, 2023 12:07 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Transformation of volume images
External Email - Use Caution
Dear developers,
please, may I ask you how I can transform volume images (containing discrete
region labels) from the fsaverage space into the space of a given subject, and
vice-versa?
I tried the following command:
mri_vol2vol --interp nearest --mov fsaverage/mri/aseg.mgz --o test_mask.mgz
--s test001 --targ
test001/mri/orig.mg<http://secure-web.cisco.com/18zhLs0yyoi6f5anIfeKiN-F1VEbpNHEjEygu8DCPePRRMe1a3jx4QEHAQ7kD_9NgtssMozXqNUTsjOs3jetomLFaKKS-TYrPODLjsmg6Jmvr-aDKJqlzzUUe-jWpXBt3EFFRhzHq-Tc1ygK4OuWuBUFXy3BgX798ZqnJB9ANvNFzdNLeovYy2s85mZfEvst-LB_nhkwwcYuCNbr1yBBmQu84PEvvUWVyYyUimGmdsWn1SuLZnAY76EMn_fL_M4OkhiBDqR30lKic7hwf72E2bNtoJVIoesBrzh8yguobZBnBN9gxTN0r-Umzvr7yFHFp/http%3A%2F%2Forig.mg>
or
mri_vol2vol --interp nearest --mov fsaverage/mri/aseg.mgz --o test_mask.mgz
--targ test001/mri/T1.mgz --lta test001/mri/transforms/talairach.lta --m3z
talairach.m3z
--s test001
but there was always a large mismatch between the transformed images and the
target image.
Best regards,
Peter
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