Hi Nan, To view multiple surfaces and surface views in one window, I suggest you switch from Caret5 to Connectome Workbench, which has many features not available in Caret.
Start by downloading Workbench: http://www.humanconnectome.org/connectome/get-connectome-workbench.html Import your Caret5 files into Workbench using wb_import, which can convert coord/topo files into *.surf.gii GIFTI files, *paint files into *label.nii files, and Caret *foci files into Workbench *foci files. Set up appropriate tabs, then use the montage view to see left and right surfaces seen from both lateral and medial views. Workbench won't draw the arrows, but hopefully you can do that part in Photoshop or PowerPoint. To identify a particular focus or pair of foci, I suggest you modify your foci file using a text editor to give the coordinates of interest a suitable foci name so that they can by easily highlighted. David On Jul 10, 2013, at 1:47 PM, Nan Xu <n...@cornell.edu> wrote: > Hi Donna, > > Thank you very much for your prompt reply and help information. > 1. However, in terms of Foci Name, I have a lot of ROIs share the same name > though they have different spatial locations. Here's my .foci file and > .focicolor file. Basically, one foci name corresponds to one color, and > several ROIs might have the same color. Thus, I failed to find a specific ROI > by searching its name. I wonder how to highlight a certain ROI by giving the > information of its spatial location. > > 2. I know how to show both left and right brain on caret, but the problem is > how to show the left medial brain and left lateral brain as well as the right > medial and right lateral on the same graph. It seems that I cannot show two > left brain spec. files(one shows the medial side whereas the other shows the > lateral side) simultaneously. I wonder if there's a way to do that, since I > try to draw arrows from one ROI which might be on left medial to another ROI > which might be on the left lateral side. > > 3. That software looks quite helpful. I will study for it! > > Thanks a lot! > Nan > > On Wed, Jul 10, 2013 at 11:09 AM, Donna Dierker <do...@brainvis.wustl.edu> > wrote: > Hi Nan, > > 1. Identifying a focus or two among a forest of foci: If you know the name > of the focus, you use D/C: page dropdown = Foci Name to toggle all off, then > toggle on just the ones you want. If you don't know their names, then you > can save the foci file as a csv file and use a spreadsheet or other sort > utility to sort on the x, y, or z position field. This will make it easier > to find the focus that corresponds to your special location. Then use the > name value in that row to toggle on just the focus (or two) that you want. > > 2. Making both hemispheres appear in the same caret window (these > instructions courtesy of Tara Smyser, who said she got them from Jim > Alexopoulos): > > a. Load the first hemisphere > b. Load the second hemisphere. During this load a window will pop up with a > button that asks whether you want to keep the initial loaded spec file. Click > on this button. > c. You will then see the second hemisphere you loaded in the caret window. > At the top of this window there is the Model drop down menu. Click on this > drop down and select the All Fiducial Surfaces Tab. This will display both > hemispheres in the same window. > > 3. Getting connections to display from one focus to another: I don't know > how to do this. Someone told me you can use vector files to do this, but > that is the extent of my knowledge. This BrainNet Viewer looks specifically > designed for that purpose, but I know nothing more about it than what this > page shows: > > http://www.nitrc.org/projects/bnv/ > > Donna > > > On Jul 9, 2013, at 5:55 PM, Nan Xu <n...@cornell.edu> wrote: > > > Hi all, > > > > I am currently made several caret plots with ROIs on the brain as attached > > files. Right now, I am trying to draw arrows from one ROI to another ROI to > > show the signal transmission. I only know the special location of these two > > ROIs, but have trouble to identify them on the caret plot. Also, I really > > hope to see the medial and lateral of left brain and the medial and lateral > > of right brain appear on the same caret graph, so that I can draw arrows > > from an ROI of medial left brain to the ROI of lateral right brain. > > > > Does anyone know how to do this on caret? at least how to identify the > > ROI's special location on caret plot? > > > > Thanks a lot! > > Nan > > <M.jpg><L.jpg>_______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > <sample.foci><sample.focicolor>_______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users
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