External Email - Use Caution the space in which the image was aqcuired.
Am Fr., 6. März 2020 um 18:31 Uhr schrieb Douglas N. Greve < dgr...@mgh.harvard.edu>: > what is "native space"? > > On 3/6/2020 12:09 PM, Benjamin Ineichen wrote: > > External Email - Use Caution > example.mgz is just some example mask created on a template in native > space. And I would need to transform it to MNI space. Thus, I ran: > mri_vol2vol --talres 1 --interp nearest --mov example.mgz --s 001.mgz > --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o > example.mni305.mgz > > The transformed mask (example.mni305) is located in a completely different > brain region in the MNI template compared to the native mask in the native > template (see screenshots). How I can I correct this? Do I need to register > the native and MNI template first? > > Thanks! > > /Ben > > Am Fr., 6. März 2020 um 17:59 Uhr schrieb Douglas N. Greve < > dgr...@mgh.harvard.edu>: > >> What is example.mgz? >> >> If you want to transfer the orig.mgz, you can do it with >> mri_vol2vol --tal --talres 1 --interp nearest --mov orig.mgz --s subject >> --o example.mni305.mgz >> >> >> >> On 2/20/2020 3:53 PM, Benjamin Ineichen wrote: >> >> External Email - Use Caution >> Dear Freesurfer experts, >> >> In order to transform a segmentation mask (example.mgz) from native so >> standard MNI space I ran: >> mri_vol2vol --talres 1 --interp nearest --mov example.mgz --s 001.mgz >> --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o >> example.mni305.mgz >> >> the output example.mni305.mgz did somehow transform to a different space >> as you can see in Screenshot orig where the native mask is white and the >> transformed mask is red. However, the masks seems to be in a >> completely different brain region in the native MNI space (Screenshot MNI). >> But the point of transforming my segmentation mask is that the segmented >> mask should be in the same brain region but just transformed to the >> standard space. How can I correct this? >> >> Many thanks for the support! >> >> /Ben >> >> -- >> ____________________________________ >> Benjamin Victor Ineichen, MD PhD >> Karolinska Institutet >> Center for Molecular Medicine >> Stockholm, Sweden >> ineic...@protonmail.ch >> +41 76 391 04 01 >> >> Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen >> Karolinska Institutet >> Center for Molecular Medicine >> Stockholm, Sweden >> ineic...@protonmail.ch >> +41 76 391 04 01 >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > ____________________________________ > Benjamin Victor Ineichen, MD PhD > Karolinska Institutet > Center for Molecular Medicine > Stockholm, Sweden > ineic...@protonmail.ch > +41 76 391 04 01 > > Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen > Karolinska Institutet > Center for Molecular Medicine > Stockholm, Sweden > ineic...@protonmail.ch > +41 76 391 04 01 > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineic...@protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineic...@protonmail.ch +41 76 391 04 01
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