Hi Emily,

> I was wondering about a few things. I know that
> you can adjust the seed radius. Is it possible to
> visualize the seed on the afni gui, so I can see
> where the seed radius extends too and do a visual
> inspection?

Not interactively, but you can easily do so with the program 3dUndump with something like:
3dUndump -master ~/abin/MNI_caez_N27+tlrc -xyz -orient RAI -prefix amyROIs amycoords.1D

where amycoords.1D contains these two lines:
18 8 -12 1 5
-28 8 -12 1 5


Also, is it possible to combine both
> left and right amygdala into a single
> correlational analysis. since I am less interested
> in symmetry and don't really have any hypotheses
> about symmetry for this data set?
Sure you can get your seed time series from any ROI even if it is not formed of contiguous voxels, but not interactively.
>
> I read that it is possible to use 3dTcorr1D to
> automate the process. I don't totally understand
> how this works. I would input the errts data set
> as the "x set." How do I tell the program what
> seed region I plan to use and can I combine seeds
> like left and right amygdala?

Use the program 3dmaskave to generate the average time series from the errts dataset using the amyROIs mask generated above. You'll want to use the -q option in 3dmaskave so that you only get the average time series out. See the example in the output of 3dmaskave -h_view

cheers,
Ziad


Would it be possible
> to look at a sample script?
>
> Thank you so much!
>
> Emily