Howdy-


>> Yes, I am running full probabilistic tractography. So, I should still be able to see the voxels of white matter connecting the basolateral amygdala with the ventromedial prefrontal cortex right?

Correct.

>> *Right now, even when I went into Object Controller, selected All Objs and then toggled to NET_000_ROI_001_002+orig and pressed the v under volume rendering, I still just get the same image of the FA image with and the representation of your '-gdset SET' is the yellow sphere+labels+connecting line (the color of the line is the matrix element value being represented).

That does surprise me. I wonder if it's just colored in dark grey as default and hard to see? You can change the color in the same controller panel. If you move to the bottom-right of the color bar, there should be a little 'Cmp'-- right click on it, and select a different color scheme from the list that appears. Any luck seeing the tract now? (Be sure to navigate around/rotate the volume a bit to make sure it's not hidding by FA slices).

If you want to not see the '-gdset SET' temporarily (but you still want it loaded to view at some point), then you can bring up the SET in the controller window (cycling through with the little arrow keys at the top), and raise the slider to the left of the colorbar all the way up-- you're setting the threshold so high that no connection should appear.


>> Even if I don't formally have a tract, I should be able to see the white matter that is connecting these two ROIs correct? Perhaps it is a matter of changing it so that the NET_000_ROI_001_002+orig file is colored so I can see it? I just basically want to do some quality checking and make sure it is connecting my 2 ROIs.

Sounds good. Visualizing data is *always* a smart idea. To visualize your target ROIs, you can also go to their controller panel and make them into volumes, and color them.


>> *Then if it looks okay, I can simply use the FA value derived for each individual for my group analysis (I can keep in diffusion space)?

Yep. And mean FA of the tracts should be mean FA of the tracts in any space. If you're using equivalent targets in each subject's diffusion space, then you should be good to go.

If you have larger networks of targets on any study, I encourage you to look at the FATMVM_DEMO, which describes some commandline tools to help take FATCAT output into multivariate modeling using Gang Chen's 3dMVM:
[afni.nimh.nih.gov]


--pt