Hi Long, Oh, okay. You mean this paper, where Alex detects areal boundaries using functional connectivity:
http://dx.doi.org/10.1016/j.neuroimage.2008.01.066 This is a legitimate use of a flat map, although I think that Alex Cohen may have figured out a way of using the spherical map, instead. Over time, he has simplified this process. Alex is a caret-users subscriber, but I forward this reply to him, to make sure he sees it. The activation map for each subject is generated in volume-land. The 2D image analysis (edge detection, etc.) is better answered by Alex directly. But let me describe one way you could create the seeds: 1. Load flat map in main Caret window. Load fiducial surface in Window 2. 2. Select Layers: Borders: Create Cartesian Grid Flat borders and enter the desired spacing. 3. Select Layers: Borders: Project borders. 4. Select File: Save Data File: Border Files - Surface: Associated surface -- change from Flat to Fiducial. The resulting border file can be opened in a text editor and/or read in by a program like Matlab. It contains a bunch of border points that represent this grid on the flat map projected onto the fiducial -- i.e., the grid all crumpled up the way the cortex actually is. Like I said, it is possible Alex is doing this on the PALS_B12 sphere now (using fiducial surfaces that have been resampled to the standard mesh, but still look pretty much identical to the native mesh ones in geometry). At any rate, there is no need to capture the flat map as an image, nor any involvement with the Brodmann parcellation whatsoever. On the contrary, if you do what Alex does, it is probably INSTEAD OF Brodmann areas (although it would be fun to compare). Donna On 07/09/2009 09:35 AM, Long wrote: > Dear Donna, > > Thank you for your quickly reply. My main purpose is to analyze the > cerebral cortex by using fMRI data in 2D way. Just like your group did > in paper: Defining functional areas in individual human brains using > resting functional connectivity MRI. Neuroimage. 2008. How to create > seeds and after calculating, how to create a 'activation map' on a > flatten cortex and perform the 2D image analysis. > > Thanks for your help. > Long > > On Thu, Jul 9, 2009 at 3:05 PM, Donna Dierker > <[email protected] <mailto:[email protected]>> wrote: > > On 07/09/2009 06:30 AM, Long wrote: > > Dear caret-users, > > I want to analyze the flatten image as a 2D image, so there > are a series of questions about this: > > 1) How to export a flatten cortex as a 2D image? So I can use > some 2D image processing methods. > > I might misunderstand you, but I think it is as simple as > displaying the flat map in the main Caret window and doing File: > Capture Image of Window. > > > 2) If a cortex was flattened, how to use the new reference > coordinate system in 2D cortex to identify the 3D coordinates, > e.g., MNI coordinates? > > In Caret, one typically would have a single topology file for all > "CLOSED" surface configurations (e.g., fiducial/midthickness; > inflated; spherical), and a CUT topology file for any flat ones. > The topology files store the neighbor relationships between the > nodes, so you can see why a flat surface, which has cuts, would > differ in its neighbors from a surface with no cuts, like the > midthickness. But each of these different configurations -- > fiducial, inflated, spherical, flat -- has its own coordinate > (.coord) file. By default, Caret writes these coord files as > binary; however, you can change the default to write them as > ASCII, so you can read in the coords into Matlab or whatever > software you like. > > If written in ASCII, the coord file will always have the node > number in the first column, so you can grep or join the 2D (flat > coord) and 3D (fiducial coord) files by the node number. See > > http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#coordFile > for more information about the coord file format. > > What is the relationship between 2D and 3D cortex. > > It is not a simple one, like an equation. Besides 2D having cuts > (broken neighbor relationships), the nodes have been projected > onto a Z=0 plane and then morphed across five cycles to reduce > distortion and crossovers. But the node correspondence remains > the same across configurations. > > It seems like you might want to do something like this: > > 1. click on the 2D image > 2. find the closest node on the 2D coord > 3. lookup up the corresponding 3D coordinate in the fiducial coord > > This is easy in Caret, and if you have flat surface in main > window, fiducial in window 2, Caret will print the fiducial 3D > coordinate in the ID window whenever you click on a node in the > flat surface (main window). > > But once you export the flat to a 2D image, rather than remain in > Caret, which is node-aware, you will have trouble getting from > step 1 to step 2 above. > > > 3) How to export one or two flatten Brodmann areas based on > the Brodmann template as a 2D image? > > This requires registering your individual subjects to the PALS_B12 > atlas, so you can deform the atlas Brodmann paint file to your > subjects' flat maps. Alternatively, you can deform any measure of > interest from your subjects to the PALS_B12 atlas, and look at the > Brodmann regions on the atlas flat map, which has a standard > shape/outline (see attached capture). > > Be aware of distortions in the flat maps -- compression near the > center, expansion at the edges. We tend NOT to use them for > measurement/statistical purposes; rather, they are handy for > drawing borders and displaying an image of the entire cortex in > one view. I wonder how you will be using them. > > > Thanks for your help. > Long > > ------------------------------------------------------------------------ > > _______________________________________________ > 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
