Hi Doug, Thanks for the quick reply. A few more details:

What do you mean by "position" (AC/PC)? Do you mean the col, row,

slice? We don't find the actual AC or PC. Yes: 3D coordinates in any identified coordinate systems. For now, we are asking our users to mark those points manually. It would be great to skip that step and have those points placed automatically. We could get the AC point from the linear Talairach transform. To transform the TalXYZ=(0,0,0) for AC to the coordinate system of the surfaces (for instance: lh.pial), should I take the translation found in the file "talairach.xfm" (4th column) ?

What file should I read to get the labels corresponding to the

aseg.mgz file? > $FREESURFER_HOME/ASegStatsLUT.txt Is there a file in the segmentation folder I could read it from? We are typically using the results of freesurfer segmentation on computers where FS is not installed...

Is there an easy way to generate surfaces for all the regions

defined in aseg.mgz? Ok, mri_tesselate + mris_smooth work well for what I'm doing.

Thanks Francois