This shows the new [July 2001] ability of AFNI to render brain structures from the Talairach-Tournoux atlas. Shown are the hippocampus, amygdala, lateral globus pallidus, and thalamus (in yellow, blue, green, and pink).

The Wedge

Here is the control panel that was used to automate the production of the above images. Note the use of two slanted cutouts and their combination with AND:

Notice that the data range was 0..594, but that Bot..Top have been set to 0..128. This is because there are very few voxels above magnitude 128 (all of them are represented in the last bin poking up at the far right edge of the histogram). The two bumps in the middle of the histogram correspond to gray and white matter respectively, in this T1-weighted SPGR dataset. The opacity graph has been set to 0 for values well below the gray matter peak, so that the small values outside the head will be transparent. The brightness graph has been set to ramp from black to white over a range that encompasses the gray and white matter. This setting is partly a matter of experimentation to produce good looking images--you want good brightness separation between the gray and white matter, but you don't want the gray matter too dark.

After this Automate run was finished, the images were saved using the "Save:bkg" button (on the image viewing window--not shown) to files wedge.*.pnm. These were converted to the GIF movie above using the csh script gmovie from the AFNI source code distribution.

Script gmovie uses programs whirlgif and ppmtogif. The source code for program whirlgif is included with the AFNI distribution, but it is not compiled in the default builds -- you must do make whirlgif to create the binary for your system. The source code for program ppmtogif is part of the netpbm distribution, which is available at many source code sites on the Web.

The Slice

Can you guess how this was done? [Hint: 2 cutouts combined with OR.]

Rotating Slice

This was done with the control panel setup pictured below (of course, you can't see the entire expression for the cutout, but I'm sure you can figure out what it was):

ShowThru Rendering

[10 Jan 2000] This shows the new "ShowThru" rendering capability, where the color overlay shows through the grayscale background no matter how deeply it is buried. In combination with animation, it is an effective way to see all the function at once.