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]> > *To:* "Caret, SureFit, and SuMS software users" > <[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 >n > > 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]> > > 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
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