Hello,

considering the surface 'lh.pial' of the reconAll process:

When I apply 'mris_convert' in order to convert to .vtk, there is a shift with respect to the .pial file when viewing in freeview.
When using the --cras_correction option for converting, the shift is gone. Nevertheless, the displayed

vertex RAS coordinates in Freeview are different. Can anyone explain that? Respectively, what is '--cras_correction'actually doing?

Moreover, when using the function 'read_surf()' in MATLAB to read 'lh.pial' I obtain the vertex coords, but when I compare
the vertex with index 1923 to the corresponding "Vertex RAS" in tksurfer, there is a slightly mismatch.

Can someone explain this? (I considered that MATLAB starts at index 1 and tksurfer at index 0!) I read, that tksurfer is actually displaying the coordinates

of the 'orig' file and not the coords of the file which is actually visible? is that true?

So the main questions are:

- What are the coordinates of the 'lh.pial' file? (surface RAS / tkrRAS, or something different?)

- Why and how do these coordinates change when converting (mris_convert) or reading in MATLAB (read_surf)?

- Is vertex with index 1000, the same after mris_convert (vtk) and read_surf()?

- Why there is a mismatch between the coordinates of a certain vertex in tksurfer and after read_surf

- Does label2label only work with tkrRAS coordinates?

Thank you very much!!