Luke,
A quick answer (w/o looking into it too much): does:
mris_info rh.pial
give you the info you need? what i'm not sure of is whether everything you see in that output is available in the structure that the matlab surface reader loads.
Nick
On Wed, 2012-11-07 at 09:17 -0500, Luke Bloy wrote:
Hi all,
I’m not sure where the best place to make this request is… so I thought I’ll put this here.
I often use freesurfer generated surfaces and images in other software packages (Slicer, Matlab etc) for various things. The MGZ files include the origin in the file headers, meaning that software can correctly interpret the world spaces of these images, allowing correct overlays with other results computed from the same scans. The problem is that the surface files treat the 128,128,128 voxel ( of the T1.mgz and other images) as the origin. But the world coordinates of this origin are, to my knowledge not in the surface files.
This creates the situation that to correctly interpret these surfaces in relation to other coordinates systems, basically I either need to ignore the world coordinates and do some registration, or I need to load both an mgz file (to get the origin) and surface files to learn correct world coordinates of the surfaces. Ideally it seems like this information should be included in the surface files themselves.
Hopefully my description of the problem makes some sense.
Thanks.
Luke
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