[caret-users] How to export flatten image as a 2D image?

[Donna Dierker]

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
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