Doug,
I'm trying to do the same thing as Ben, i.e., show a FS surface (e.g. 'lh.white') in the same space as the MRI ('T1.mgz'). I have been studying the wiki page (and linked PDF) but I'm a bit lost. Is there an easy way to get an affine transform that maps the surface to the coordinate system the MRI volume uses? I know there has to be but it is not clear from the wiki page where I would find this information.
Ben: Have a look at mne-python [1] or or also this PySurfer example: http://pysurfer.github.com/examples/plot_meg_inverse_solution.html
It shows you how to display MEG/EEG activity on the inflated surface but you can also use pial. There is also a little GUI that lets you change the time point and color map.
[1] http://martinos.org/mne/mne-python.html
Best,
Martin
On 02/28/13 14:26, Douglas N Greve wrote:
Hi Ben, there are several things going on/wrong here. tksurfer reports the coords from the orig surface (historical reasons) which will be slightly different than the white surface in most casesand somewhat different than the pial. These coordinates are in our special coordinate system and not scanner RAS. To get RAS, see http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
doug
On 02/28/2013 02:21 PM, Brinkmann, Benjamin H., Ph.D. wrote:
Dear FreeSurfers,
I am working on generating a functional map of electrophysiological activity on a freesurfer pial surface and I've come across something that has stumped me. I have the electrode coordinates in RAS space and I am trying to interpolate a value at each surface vertex for the color map using the RAS coordinate of each vertex. However, the RAS coordinates I read into matlab using freesurfer_read_surf.m are different from what is being displayed in tksurfer. (I'm comparing RAS coordinates by hovering the cursor in tksurfer.) Most of the time the differences are very small, but occasionally they can be large. I haven't been able to identify any kind of a constant offset or relationship between these coordinates.
Should the RAS coordinates displayed in tksurfer be the same as what is read directly from the surface file? Is there a better way to approach this task?
Thanks very much for any suggestions.
Regards,
Ben Brinkmann
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Benjamin H. Brinkmann, PhD Mayo Systems Electrophysiology Lab Alfred 9-441C, SMH 1216 Second St. SW Rochester, MN 55902
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