On 10/29/2009 02:39 PM, Danny Kim wrote: > Hi fellow caret users, > > This is my first time posting a question to the mailing list. Forgive > me if I leave out anything important or formality. I'll try to include > everything I know. > > so I've been trying to landmark and paint the sulci of this brain (see > attached photos of Lateral and Medial view of resulted fiducial and > inflated surfaces). Well, it's almost Halloween, so I guess scary images are seasonally appropriate. But I must say, that is a pretty hideous fiducial surface you have there -- lots of appendages and handle-like spindles. Did you tessellate something like a FSL fast segmentation? > > I keep getting paint Sul.CeS not found and the automatic landmark > labeling does not go to finish in surefit segmentation. I just got that error today myself. In my case, it was because I was running auto-landmarks and feeding it a bad Depth column-name/number. But you might also see that error if your spec file has more than one anatomical volume in it. It just always seems to be that error whenever auto-landmarks fails.
In your case, I can't be sure what caused it to fail. It could be that your surface isn't in 711-2B stereotaxic space. Eventually, we'd like to add handling to make the process of getting surfaces into 711-2B more seemless. But we're not there yet. But really you're going to have to improve the quality of the segmentation that generated this surface before registeration makes sense. > > How does the automatic paint generation of the core6 landmark, and > other sulci labels actually work? By my understanding, Caret, once it > finds the sylvian fissure correctly, should be able to locate the > central sulcus shouldn't it? and after that it should find all the > other sulci paints by using the B12 atlas. This isn't really documented/published anywhere, as far as I know. I'll give you my oversimplified take on it: The surface must be in 711-2B, so that the probabilistic volumes in your $CARET_HOME/data_files/sulcal_identification directory align properly with it. Several ROI volumes (e.g., CeS, HF, SF) are mapped to the surface, thereby forming surface ROIs, which are intersected with thresholded Depth metrics to pinpoint the location of key anatomical structures. Borders are drawn and trimmed to our Core 6 landmark specifications. > thank you all for any suggestion/input/critique! > > > Cheers, > > Danny Kim > Brainmapping > Dept. of Neurology > BC Children's Hospital > Vancouver, BC > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > 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
