Hi-

Let's say you have an atlas or ROI map DSET_ROI where the amygdala is defined wherever that dataset has a value 4, and it could also have a label attached like "Amygdala". You can use the "-mask .." option and sub-range selector to focus on just that ROI and its time series:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/afni_gen/files_gen.html#sub-range-selection
... getting its eigenvectors (=PCs).

For example, if you have DSET_4D as your time series dataset, then this might be one option, using sub-range selection:

3dpc -dmean -nscale -pcsave 1 -float -mask DSET_ROI"<4>" -prefix OUTPUT DSET_4D

or, if "3dinfo -is_atlas_or_labeltable DSET_ROI" outputs a 1 and, as noted above, there is a label "Amygdala" associated with the ROI with value=4, then:

3dpc -dmean -nscale -pcsave 1 -float -mask DSET_ROI"<Amygdala>" -prefix OUTPUT DSET_4D

should produce the same output.

To get the eigenvectors/PCs from the ROI, you would *not* want to first collapse the time series within that dset to an average. That would remove the ability to decompose the time series into PCs.

--pt