Hi all,

I have a similar problem using Paraview:
When I visualize the surface lh.pial and the anatomical image brainmask.mgz using FreeView they nicely overlap; however, after I convert lh.pial to lh.pial.vtk and brainmask.mgz to brainmask.mha and visualize them using Paraview, they are in different spaces.

Do I need to apply a transformation matrix to lh.pial using the command line mri_surf2surf so the VTK surface will overlap with the image when using Paraview?

I find this quite confusing.

Thanks!

Kindly,

Islem

On Tue, Aug 30, 2016 at 9:21 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

tksurfer always uses the ?h.orig coordinates. Also keep in mind that the vertex index is 0-based whereas matlab is 1-based. When you click on a point, you should see something like the following print out

selected vertex 123491 out of 163842
current -39.11 15.65 11.26
orig     -55.67 -10.37 19.95
pial       0.00   0.00   0.00
white    -55.76 -10.29 19.93

On 8/30/16 5:12 AM, Dongnandi wrote:
Dear Experts,

I tried to extract vertex coordinates information from ‘fsaverage/surf/lh.pial’ file using matlab function ‘read_surf’, but I found that the coordinates returned by the function are different from what I saw in tksurfer, here are the screenshots:

The vertex index starts from 0 in tksurfer, so I select the second elements in matlab. Why is the result different from what has been shown in tksurfer(also different in freeview)? Which one should I report?

Is there any way to transform the surface coordinates to the MNI152 space?

Thank you very much!

Dong
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