Taosheng, I don't think there are any tutorials for doing what you want to do. We had a tutorial for registering Freesurfer data, but it's pretty outdated. We have scripts that are more helpful for that, and you may end up adapting those.
It is possible to generate inflated, very inflated, ellipsoid, and spherical surfaces using Surface: Geometry: Generate inflated (etc.) from fiducial. Then in principle, you could use these inputs for registration purposes. In practice, we smooth the medial wall before registering our subjects, which means drawing a border around it (or using auto-landmarks to do so); smoothing just the encircled nodes; and then regenerating the inflated, very inflated, and sphere using the fiducial with the smoothed medial wall. Depending on your purposes and how many subjects you have, you could skip this step. It used to be that you could draw borders only on 2D surfaces (i.e., flat). But now that you can draw on 3D surfaces, flattening can be bypassed. Have a look at the scripts described in this post: http://www.mail-archive.com/[email protected]/msg01831.html Even if you don't think you need scripts for your purpose, at least you can see the steps we use to register Freesurfer-generated data, and if there is something you don't understand, you can ask about it. Donna On 10/15/2009 09:12 AM, Taosheng Liu wrote: > Hello, > I'm new to Caret and I'd like to run spherical registration to the > atlas and do group analysis. Most of my analysis is done in custom > Matlab codes. I use a combination of FreeSurfer and SurfRelax (a less > used software) to do segmentation and surface recon. > I'm able to output my surface to Caret fomat, i.e., I can generate > topo and coords files for a folded hemisphere, and open/visualize them > in Caret. I tried to follow the Caret_5.5_Tutorial_Segment.pdf for doing > registration, but I'm currently stuck, because it seems to require > flattened/inflated/spherical surfaces of my subjects. > I'm imagining that I can start with my folded surface and do all those > things, and then follow the tutorial to do spherical registration? My > question for now is simply: is this the right approach? If so, can > someone tell me how to start with a folded surface to generate the > Inflated, Ellipsoid surfaces, etc., that are normally generated during > the segmentation process in Caret? (e.g., the surfaces shown in Fig. 34 > in the tutorial) I looked in the menus but couldn't find anything. > Thank you very much, > > --Taosheng Liu > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
