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Hi Douglas, thanks for your suggestion! However, the result is not very accurate. This is, what I did: 1) I had calculated a reconstruction for the colin27 image by execution of the complete "recon-all all" procedure. 2) cd colin27/mri mri_convert -at transforms/talairach.m3z orig.mgz colin27_in_fsaverage.mgz freeview -v colin27_in_fsaverage.mgz -v ../../fsaverage/mri/aseg.mgz -> See colin27_aseg_in_fsaverage.png E.g. the ventricles and cortex do not match very well. 3) Overlay of the files which were generated by recon-all: freeview -v orig.mgz -v ./aseg.mgz -> See colin27_aseg_in_orig_space.png Both, the MR image and aseg match very well.
So I think that aseg.mgz was transformed differently by recon-all. Please, could you help me find out, which steps are necessary for this transformation?
I want to use this to transform our atlas (which is in the colin27-space) into the fsaverage-space, so that it can be used for the regional analysis.
Best regards, Peter
On Wed, Nov 22, 2023 at 7:09 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
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 CautionHi 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1aYcHMAkFe1OK3WK3VP7G4IQRAE7SMA4TynV9AQTu1rmyVW... 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.mgzIn 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 nearestBest,
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 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,
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