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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