For some reason, after simplification, caret does not recognize the simplified surface as a fiducial surface. So, save the simplified surface as fiducial coordinate and closed topology files, exit Caret, and restart Caret. Restart the mapping process and you should be able to select Map to Caret.
Note that the map volume to surface process maps voxel data to the surface nodes. With a simplified surface you have fewer nodes and it is possible that an activation may fail to map to the surface where there are no nodes. On Mar 25, 2010, at 10:13 AM, Figa Pelosa wrote: >> If you have individual data, you could simplify the >> individual's surface and then map the functional data to >> it. > > I'd actually need to map the fMRI data directly on the simplified mesh: If I > FIRST map the data on the PALS surface, and THEN simplify the mesh, I've got > these problems: > > 1) After the mesh simplification, the colours on the mesh (the mapping of the > fMRI data) are gone. Furthermore, nothing happens if I change the "primary > overlay" settings. > > 2) If I load the fMRI data again, trying a new mapping from scratch, it is > not possible to choose the "Map to Caret" option: I'm forced to use "Map to > Caret With Atlas". > > 3) If I do so, and choose "metric" in the primary overlay, I've got a message > (in the linux shell) saying "Metric file has different number of nodes than > the surface." and nothing happens. > > In summary, what I'd need is one of the following possibilities: > > 1) To map the fMRI data on the PALS surface, then simplify the surface and > still be able to see, and save on file, the mapping (on the simplified > surface). > > 2) To simplify the PALS surface and use it as an atlas (i.e., instead of the > PALS surface) > > Thanks a lot for your help > Ale > > > > > > --- Gio 25/3/10, John Harwell <[email protected]> ha scritto: > >> Da: John Harwell <[email protected]> >> Oggetto: Re: [caret-users] simplified meshes >> A: "Caret, SureFit, and SuMS software users" <[email protected]> >> Data: Giovedì 25 marzo 2010, 13:47 >> >> Hello Alex, >> >> Why do you need a simplified surface? >> >> If you want to map the PALS atlas you will not be able to >> use a simplified surface. The PALS atlas contains two >> methods for mapping functional volumes, AFM (average >> fiducial mapping) and MFM (multi-fiducial mapping). We >> recommend using MFM which maps the functional volume to 12 >> surfaces and then outputs metric data that is the average of >> the 12 mappings. >> >> If you have individual data, you could simplify the >> individual's surface and then map the functional data to >> it. >> >> In summary, use PALS as it is. >> >> John >> >> >> >> On Mar 25, 2010, at 5:53 AM, Figa Pelosa wrote: >> >>> hello, >>> my name is Alex and I'm trying to map an fMRI volume >> on a simplified version of the >> "Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730" >> surface. >>> >>> Till now I only managed to simplify the surface, using >> Surface->Simplify surface. >>> >>> What I'd like to do is to save all the info I need >> (e.g. files such as .metric, .coord, .topo, ...) to be able >> to use the simplified surface as it was the original >> suface. >>> >>> Could somebody teach me how to do that? >>> Thanks a lot >>> Alex >>> >>> >>> >>> >>> _______________________________________________ >>> 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 >> > > > > > _______________________________________________ > 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
