> To visualize my tract (basolateral amygdala to vmPFC, with the centromedial amygdala as an exclusion mask, I used the following:
> $ suma -vol PAIRMAP_NAME[0] -gdset o.PR_000.niml.dset -vol FA_FILE

So, I'm *guessing* that you're running probabilistic tractography ('-mode PROB'). Therefore, no *.tract file gets output, only volumes.

> However, I ran into the following error: Error SUMA_LoadDsetOntoSO_eng (SUMA_Color.c:10118):
> Could not find network_file "o.PR_000.niml.tract" on disk for dset
> The o.PR_000.niml.tract was not created.

Right, so something internally, for the created *niml.dsets, for DET and MINIP modes, one can view the tract bundles colored by matrix values-- like viewing the connectivity matrix colored for the connections in 3D in SUMA. However, there's a minor wrinkle, that this only works for MINIP and DET mode where tract files are created-- the error message you get should not be terminal (though, I admit it is not something that should be happening). I am guessing that you can still open SUMA and view stuff? THis should be not a terminal error, and we'll have to decide how to deal with this when outputting *.niml.dset files in PROB tracking mode (and also in 3dNetCorr, if no tracking has been run, actually, but that's another story). Bottom line: if this specific message is currently not terminal, don't worry-- we'll fix the message/compatability.

> Also, I did use the -dump_rois AFNI and I did NOT have a NET_000_ROI_001_002+orig. created. I see that I have created a NET_000_ROI_001_001+orig and NET_000_ROI_002_002+orig.

This does surprise me. Is there a tract connection found between the target ROIs labelled with a 1 and 2? Can you seen on in the PAIRMAP file? If so, can you please copy the command being run here? If you *don't* see that connection in the PAIRMAP files either, then that means it wasn't found-- you can also check the *.grid file, and see if there is a nonzero matrix element in the spot for the 001 and 002 connection.

--pt