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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