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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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

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