coordinate scale problem

[ChenK19]

hello, i am dealing with the seeg signal and get the coordinate from freesurfer. However, when i visualize these coordinates with your toolbox, i found some electrodes coordinate outside the borderline of your brain model(especially for the occipital lobe, far away from the brain borderline).

could you please give me some advice on how to debug it?

[StuartJO]

You'll need to double check all the coordinates are in the right space. The coordinates of the vertices I provide are taken directly from ?h.white or ?h.inflated from fsaverage. Check if you are using subject specific coordinates because those are unlikely to align with fsaverage. In that case you'll need to use each subjects own ?h.white/?h.pial (won't work with the inflated space) to insure the electrode coordinates are in the correct reference frame.

[ChenK19]

hi, i check the source of our coordinates, it's the coordinate in the mni coordinate frame(has been transformed), will this cause some problem?, and i check the difference between "plotsurface" and other visualization toolbox, it seems to be about 20mm offset along the yaxis, which may cause my problem(offset in the oppital lobe area), but i have no idea how to deal with the "20mm" offset precisely.

Do you have any idea?

[StuartJO]

If the source coordinate is MNI then it won't correspond to the coordinates of the surface I provided because the surface is in fsaverage space. If the coordinate is transformed then double check. You can have a look here https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion too see some ways of how to get the coordinates in the same space. That is all I can really suggest!

[ChenK19]

I think i solve the problem, read directly from ?h.white or ?h.inflated from fsaverage, lh and rh are not in the same coordinate, that need a transform to merge them together.