These are files you would have if you either created an individual surface in Caret, or if you imported a Freesurfer surface into Caret.
The pipeline streamlines a lot of this process and imposes a file naming convention. I recommend it. On 01/31/2011 10:40 AM, Amy Watson wrote: > Hi Donna, > > I appreciate your reply. In the example spec file you sent, I see > topology files, coordinate files etc How can I get them or create > them?Should all these files be in the same folder as the spec file? Is > there any specific naming convention that should be used? > > Thank you, > Amy > > ------------------------------------------------------------------------ > *From:* Donna Dierker <[email protected]> > *To:* "Caret, SureFit, and SuMS software users" > <[email protected]> > *Sent:* Mon, January 31, 2011 10:26:02 AM > *Subject:* Re: [caret-users] Mapping fMRI results > > On 01/31/2011 09:36 AM, Amy Watson wrote: > > Hi Donna, > > > > Thanks so much for your reply. I just want to reconfirm one thing again: > > > > In order to map functional results onto surface, I definitely need a > > spec file (a surface in Caret format). Am I right? As you said, I can > > use the Freesurfer-to-PALS pipeline to create a spec file. Is there > > any other way to get a spec file? > There are several ways to map volumes to surface in the GUI, and I know > some (e.g., mapping to atlas) requires a spec file. I'm not certain > mapping to caret does, because to do it, you must already have a spec > file open. > > But generally you need a spec file to view the results anyway. > > You can use a text editor to create a spec file, if you want, but you > must know the right file type tags to use. See an existing spec file > for examples. You can also use spec files from tutorial datasets, like > the Sept 2006 tutorial. > > Here is an example of simple spec file contents: > > CLOSEDtopo_file Human.SAIS_003.L.CLOSED.73730.topo > FIDUCIALcoord_file deformed_Human.SAIS_003.L.Midthickness_711-2B.mws.coord > SPHERICALcoord_file > Human.SAIS_003.L.SPHERICAL.73730.MWS.SPHERE_CYCLE4.ALIGNED.coord > borderproj_file Human.SAIS_003.L.LANDMARKS.ekr.borderproj > surface_shape_file Human.SAIS_003.L.Initial.73730.surface_shape > > > > Thanks a lot, > > Amy > > > > ------------------------------------------------------------------------ > > *From:* Donna Dierker <[email protected] > <mailto:[email protected]>> > > *To:* "Caret, SureFit, and SuMS software users" > > <[email protected] <mailto:[email protected]>> > > *Sent:* Fri, January 28, 2011 9:47:29 AM > > *Subject:* Re: [caret-users] Mapping fMRI results > > > > 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 <http://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] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > caret-users mailing list > > [email protected] <mailto:[email protected]> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > [email protected] <mailto:[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
