Thanks for the reply Nick, Yes mris_info does return information I would need.
volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : ( 5.8612, -8.9756, -36.8004) file : ../mri/filled-pretess255.mgz interestingly even if I move the surface file out of the subject's surf directory it still returns this info, making me think that it is in the file somewhere. I was looking at read_surf.m last night and it doesnt seem to do anything with this info, and http://wideman-one.com/gw/brain/fs/surfacefileformats.htm doesn't mention any of this info being in the file. is there an updated spec file on the file formats? Thanks. -Luke On Wed, Nov 7, 2012 at 3:26 PM, Nick Schmansky <ni...@nmr.mgh.harvard.edu>wrote: > 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 > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
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