Re: [Freesurfer] Transformation of volume images

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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 YHUANG43@mgh.harvard.edu wrote:

Hi Peter,

Here is an example to convert from native space to MNI305 (fsaverage) in https://secure-web.cisco.com/1ReBfmWJausgcUfY96AjUCIcfqx5PX2Bs775KpxZcv9gOmT...

  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

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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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1py-tr0DLfSy2yJEGh0vV3NGEqR8Wt1hg3C_oNipLRzEoO1... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1pSyFH3poVhDMzYdvm6gsnO6iSVuIOIocPklObaavuvaYxi... < https://secure-web.cisco.com/1pSyFH3poVhDMzYdvm6gsnO6iSVuIOIocPklObaavuvaYxi... .