You can try CVS (mri_cvs_register). It will take a while to run
(typically about 12 hours), but it will be much more accurate
On 11/23/2023 4:23 AM, P Pieperhoff wrote:
External Email - Use Caution
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
<dgr...@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:
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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
<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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