On 08/30/2018 02:24 PM, M. Jordan wrote:

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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?)

tkrRAS, see https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems

• Why and how do these coordinates change when converting

(mris_convert) or reading in MATLAB (read_surf)?

In general they should not change. but if you add --to-scanner to mris_convert, then it will convert the coordinates to scanner instead of tkrRAS

• Is vertex with index 1000, the same after mris_convert (vtk) and

read_surf()?

Yes, but you need to make sure that you are taking into account that matlab is 1-based.

• Why there is a mismatch between the coordinates of a certain vertex

in tksurfer and after read_surf

tksurfer or freeview? In fv they should be the same. In tksurfer, it may be giving you coordinates for the white or orig surfaces.

• Does label2label only work with tkrRAS coordinates?

If you are using   --regmethod surface, then it does not use the coordinates at all (actually, it uses the spherical coords in the lh.sphere.reg)

Thank you very much!!

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