On 02/13/2017 09:59 AM, Ting Qi wrote: > Dear freesurfer experts, > > I have some questions about the coordinates conversion, and the relationship > between several types of coordinates. > > First of all, I’d like to confirm whether the coordinates reported in the > results summary are based on MNI305 space? Which summary? From mri_glmfit-sim? That is in MNI305 space. > > Second, I plan to combine multi-modalities data, therefore I would like to > use the peak vertex in the surface as a seed to do additional volume-based > analysis. I have the vertex index, vertex ras, MNI coordinates reported in > the summary text, but how can I get the correct and corresponding volume > coordinates in MNI space, particularly in MNI152? These are always tricky things. First run recon-all on the MNI152 brain. Next, create a surface overlay file with my target voxel = 1 and everything else 0. See https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51127.html. Map this file from fsaverage the mni152 using mri_surf2surf. Once there, map the surface into the volume space using mri_surf2vol. You can threshold it there to determine where your voxel is. > > I read the page about the freesurfer coordinate system, they mentioned > several cases about the transformation, but I still cant figure out what is > the correct way in my case. Moreover, I tried the mni305 to mni152, but when > I double checked the coordinates in mni152 space, the peak was no longer > corresponds to the region reported in the mni305 space. So I sure there must > be something wrong. > > Finally, would anyone offer me a explanation about the relationship between > surface RAS, volume RAS, MNI* RAS, Vertex MNI, Volume MNI coordinates? It > quite confused me. All of this is in the coordinate system page. If you have more questions, please ask something specific. > > Thanks in advance, > > Best regards, > Ting > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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