The coordinate system is not easy to explain in an email. There are power point slides on our wiki about the geometry used. To get from surface xyz to column, row, slice in the orig.mgz, first get a matrix from the orig.mgz with

mri_info --tkrvox2ras orig.mgz

this will be 4x4, multiply the inverse of this matrix by the surface xyz (adding a one to make it 4x1) to get the col, row, slice in the orig.

doug

f.leone@donders.ru.nl wrote:

Hi all,

I checked quite a number of previous posts, but still can't seem to figure out what the vertices numbers given by read_annotation in matlab stand for. My questions are:

• In what reference frame are they?
• How do I convert them to coordinates in my original structural image (an x * y * z matrix, based on a nii-file)?

Thanks a lot in advance!

kind regards,

        Frank