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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