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 > 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1py-tr0DLfSy2yJEGh0vV3NGEqR8Wt1hg3C_oNipLRzEoO1-3U4VGRm8OYPy-BUfh8qNXIp__UxTcax1oKzLhN-vBlwS__NrG7550TiMeeVa9lSFY_7KB6cg-9bHIzjfh57U6lu3YvswS7IoYEJUIuPD8DESRuBI8I1U9N3eaY2qRfAfzlOQ8VGHhcbx3DQvro__Du2IWyMydO5-vrDG6VXgBPn0dz2QbcLvQgOiO7ig2R3L2-TGSrM-5HY0kGDvXYYL_GZaLKV1FwRBd4bmrH0yqVMZBZodSRNTCDs8x3o8VAsoL54BM1V2evQVPQo7eF_6GQfgkDR2lvMi_1N-SDA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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/1pSyFH3poVhDMzYdvm6gsnO6iSVuIOIocPklObaavuvaYxinM134nEm05HWM9YQ2RTi5Ao8yIM5AaI7ql1hVR6GJ0XnKocnbZ3nWsENSpgLevyteHbWkuOr5-F2syMINOdJnZHqOo2i_4UZbfhaRCiolw8ppVuPIxoGza7KaJ-NvasN2Zh7gEyn87hLK0fZ2K7OpmzOkYNAsDoakT71sVZx9cug2CIrdKSE27HsRzS2Ts0V0Iig9favL_noFOgQPlcWQEknbroFcDIK6_YKz7xMmxap0ac1suWUmcupFv1YOG_8Mexiu3QBogrkvmloEFcqv2JkYqlyMRQRwMQiWWnA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1pSyFH3poVhDMzYdvm6gsnO6iSVuIOIocPklObaavuvaYxinM134nEm05HWM9YQ2RTi5Ao8yIM5AaI7ql1hVR6GJ0XnKocnbZ3nWsENSpgLevyteHbWkuOr5-F2syMINOdJnZHqOo2i_4UZbfhaRCiolw8ppVuPIxoGza7KaJ-NvasN2Zh7gEyn87hLK0fZ2K7OpmzOkYNAsDoakT71sVZx9cug2CIrdKSE27HsRzS2Ts0V0Iig9favL_noFOgQPlcWQEknbroFcDIK6_YKz7xMmxap0ac1suWUmcupFv1YOG_8Mexiu3QBogrkvmloEFcqv2JkYqlyMRQRwMQiWWnA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
