Derin,You might try importing the surfaces into Caret for this. It seems like there are two needs:
* flat cartesian grid (Menu bar: Layers: Borders: Create Cartesian Flat Analysis Grid Borders (see attached capture) * 3-D scale markers (Toolbar: D/C: Surface Miscellaneous: Surface Cartesian Axes
Here is what the scale markers look like: http://brainvis.wustl.edu/pub/donna/US/WASHINGTON/200803/views.html login pub password download Donna On 03/25/2010 11:19 AM, Bruce Fischl wrote:
sorry Derin, I just poked through the tksurfer source and can't find it. I'll try to look more thoroughly later. I think Mary (Sereno) actually wrote this code to begin with and I modified it, so you could try pinging him On Thu, 25 Mar 2010, Derin Cobia wrote:Don't have the source, but I could download it. What am I looking for? Do you think it would it be possible to do this in Matlab or something, and import in (as an overlay maybe)? New territory for me, I'm sorry too... :( -Derin On Mar 25, 2010, at 11:00 AM, Bruce Fischl wrote:Hi Derin, you could try this in tksurfer, but it isn't terribly well documented or supported (or remembered by me). I hacked some stuff together in tksurfer to get those images, but haven't used it in more than 10 years. Do you have the source? You're welcome to poke through it, but I'm not sure it works anymore. sorry for the unhelpful answer :< Bruce On Thu, 25 Mar 2010, Derin Cobia wrote:Along these same lines, is it possible to overlay/display a Cartesian grid on the surface, a la the Neuroimage '99 II paper (Fig 7)? And is it possible to specify what the 'north pole' of this coordinate system is? For example, if I wanted it to be at the posterior end of the STS. I'm looking to do this on a flat patch. Thanks. -Derin On Mar 25, 2010, at 10:34 AM, Bruce Fischl wrote:Hi Eric, in tksurfer click view->scale bar to see the 1cm bar. cheers, Bruce On Thu, 25 Mar 2010, Eric Moulton wrote:I was wondering if freesurfer has a way of generating a scale for distance, similar to what one would see in the legend of a roadmap. I'm thinking of using such a scale for a 3-d pial surface-render of an averaged brain (as generated using make_average_surface). Since it's a 3-d image, I had in mind a sort of 3D Cartesian coordinate scale, with scale bars for the x, y, and z directions. Does freesurfer have some visual representation of a distance scale like I've described, or perhaps some alternative? Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ 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._______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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