On 01/27/2011 03:01 PM, Amy Watson wrote: > Hi, > > If I want to map an individual's fMRI results (FIDL output) on his own > brain surface, should I first create the surface (say, in Freesurfer) > and then load it into Caret and use Attributes Menu -->Map Functional > Volumes to Surfaces ? Yes: To map individual data, you need a surface reconstruction of the subject's hemisphere. Freesurfer is a good way to get one. See the information about the Freesurfer to PALS pipeline here:
http://brainvis.wustl.edu/wiki/index.php/Caret:Download#Download_Freesurfer_to_PALS-B12_Pipeline_Distribution But note also that you can map functional data in Freesurfer, so there is more than one way to do what you want to do. If you use the pipeline to import your Freesurfer surface into Caret, then you would load the resulting spec file and the functional volume. Then, do Attributes: Map volume to surface and select metric. Add loaded volumes and Map to Caret. > I tried Caret's quick tutorial where in I had to select 'Map to Spec > file with Atlas' while doing the mapping... Is a spec file similar to > a surface created in Freesurfer? How can I create a spec file? I would > very much appreciate your reply. Freesurfer won't create a spec file, but the Freesurfer-to-PALS pipeline preborder.sh script will (see link above). Since you are using FIDL, I'm guessing you are at Wash U. If so, then I will be giving a NIL talk about this pipeline on 2/18 at 1:30pm. > > Another question - when I use Metrics to RGB Paint Dialog, there is a > threshold selection box where I can enter thresholds. > In the Display Control Dialog -->RGB Paint Settings Page, there is > again an option to enter threshold for Red, Green and Blue. Are both > these one and the same? No, I don't think so. And I don't think I can explain this very well, so I hope John Harwell will see this. My impression is that when you set the threshold in the Metrics to RGB dialog, then any sub-threshold signal will get 0 value from that channel, so that information effectively gets thrown away, and the supra-threshold signal has more room to spread out across the color scale. In the D/C dialog, you can suppress display of RGB signal that got past the first step, and was captured in the resulting RGB_paint, but you don't want to see it right now. And I don't think this latter option affects the scale, the way the first one might. These are guesses. As you can tell, I don't have a firm grasp on this. > > Thank you, > Amy > > ------------------------------------------------------------------------ > > _______________________________________________ > 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
