I think it's probably just displaying them in different coordinate systems. tksurfer displays in an RAS coordinate system in which (0,0,0) is essentially the center of the volume, whereas Neurolens is probably displaying scanner coordinates. Does it matter to you? Not sure I understand - is it causing you any problems?

Bruce

On Wed, 7 Jun 2006, martijn van den heuvel wrote:

Dear freesurfer-users,

I want to plot the freesurfer surface rendering (xxx.pial) in the program Neurolens. Loading the image gives no problem and Neurolens gives a beautiful rendering. However, when loading the pial surface in tksurfer I see a difference between the two renderings. The surface in tksurfer is centered to RAS (0,0,0) , like the T1.mgz image (as it supposed to do). Im trying to figure out what this translation is, but I cannot find the answer on the web, hence this email. Does tksurfer loads in a translation file (except for the talaraich.xfm, I got this translation covered), or does it do a general shift to the RAS centre? Generally, Im looking for the translation matrix from RAS to world coordinates, so I can apply this translation to the surface before loading it in Neurolens.

I hope someone can help me with this question.

Yours sincerely,

Martijn van den Heuvel