You can use something like
mri_convert orig.mgz -at mri/talairach.m3z orig-in-mni305.mgz
This is nonlinear. It takes you to the mni305 space.
On 11/21/2023 11:45 AM, P Pieperhoff wrote:
External Email - Use Caution
Hi Yujing,
thank you for your help! But I think, this is only the affine
registration?
Is it possible that I can use the same transformation, by which e.g.
aseg.mgz-atlas is transformed into the native space of a given subject?
The volume-dataset of the subcortical regions matches quite well with
the subcortical structure of each subject, but I think that this can't
be achieved by an affine transformation only.
Best regards,
Peter
On Fri, Nov 17, 2023 at 3:57 PM Huang, Yujing
<yhuan...@mgh.harvard.edu> wrote:
Hi Peter,
Here is an example to convert from native space to MNI305
(fsaverage) in *MailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2vol
<https://secure-web.cisco.com/1ReBfmWJausgcUfY96AjUCIcfqx5PX2Bs775KpxZcv9gOmTBSGzKXWFDQm3aeoDGEum66aG9yEs1oHr1_wTN6i2SvYPOCQ1sz_ZLdti5OCmdKssoz0DU5uDEd4yWNwuPoJ34VTWQlJZehHnFjRZJugcyy1Q4IkVV-FVasIrShFvpSVKNr0hcH_DWpycse2cFHlkv-BlqGkzcj-zeNCZi2giLNTyaz2EJ5KmUau7JMUjqg0vGLIFRRWlaaw_qSJtoHzr6tnk7-SPAyrntbI8Dli8oYsM2nGRZlRx-bFJnLCtgOx-ga_lgPFABOV8jAk6FvlqoxP0Kz6QHY5z6TSfb3yA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_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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