Hi Florent if you run mris_info on the surface of interest it will print out the vox2ras-tkr matrix that you can use for this conversion.
cheers Bruce On Fri, 26 Oct 2018, k3...@free.fr wrote: > External Email - Use Caution > > Hi Freesurfer team, > > Sorry to ask a new question about FreeSurfer coordinates (I know it has been > debated multiple times reading old messages) but I am still confused with all > these spaces. > I have a very simple use case in Freeview, when I load the T1.mgz image I > would need to get the "TkReg RAS" coordinate of points using the pixel > positions (last line in Cursor/Mouse coordinates in Freeview). > I know Freeview is providing the conversion but I would need to be able to > extract the "TkReg RAS" coordinates for multiple pixel positions in the > T1.mgz file. > > I've read the FreeSurfer documentation > (https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) but it is still > confused for me when I look at the coordinates in Freeview... > Which transformation is used to convert pixel coordinate (T1.mgz) to > Talairach, TKReg RAS and RAS systems? > I also found this interesting link http://brainmap.org/icbm2tal/ and > implemented the mni2tal / spm2tal / fsl2tal / other2tal transformations (in > Python/Numpy) but unfortunately none of them gave me good results. > > Thanks for your help. > > Florent > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://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
