Hi again Daniel -

Okay, I dug into the mystery of the "WamI" button in the cluster report more deeply. Unfortunately I must report that I am still confused. The biggest confusion is that in one context AFNI seems to be working appropriately wrt atlas lookups via the 'whereami' command, and in another context not. For instance, when I open the cluster report, click "Jump" on the first cluster, then go into an image window, right click, and select "Where am I?" the following logging gets printed in the console:

++ Running WamI command: 
 + /home/shanusmagnus/afni/whereami -omask ./Clust_mask+tlrc.HEAD
reading TT_caez_pmaps_18+tlrc(348 million [mega] bytes).........done
reading MNIa_caez_pmaps_18+tlrc(328 million [mega] bytes).........done
reading TT_desai_dkpmaps+tlrc(325 million [mega] bytes)........done
reading TT_desai_ddpmaps+tlrc(697 million [mega] bytes)................done
reading TT_desai_fspmaps+tlrc(186 million [mega] bytes).....done

and, after a bit of thinking, I get a giant list of atlas locations corresponding to the crosshairs. If, however, I click the "WamI" button from within the cluster report button, I get something akin to the screenshot I provided in the first message in this thread; and the console logs this:

++ Writing mask dataset ./Clust_mask+tlrc.BRIK
*+ WARNING: Over-writing dataset ./Clust_mask+tlrc.HEAD
 + 3dclust -1Dformat -nosum -1dindex 0 -1tindex 1 -2thresh -3.922 3.922 -inmask -dxyz=1 -savemask Clust_mask 1.01 10 /labs/koutstaal/Semantic_Cognition/semantic_root/worktemp/broda/abscon__b38_mni.nii.gz
++ Running WamI command: 
 + /home/shanusmagnus/afni/whereami -omask ./Clust_mask+tlrc.HEAD

I don't think the issue is AFNI_ATLAS_LIST -- when it was not explicitly set, the behavior I observe is the same; but to be sure, before performing the aforementioned steps I set it in my .afnirc to ALL. Memory is also not an issue, since the requests for "whereami" are fine when made in the display window; and I've verified by looking at the process list that there's nothing spinning and swapping.

So the question is, what's going on? Based solely on the console output it seems that the whereami launched from the cluster report is not consulting the atlases in the same way as when you invoke it from the display window. However, it should be noted that I've been assuming all this time that clicking WamI from within a cluster report would give something like the atlas locations of the contents of the clusters, and so the current behavior is faulty somehow. Is this right? I could obviously jump through the various clusters in the cluster report, mouse to a display window, right click, and select "Where am I?" to get the results for that particular voxel (and not the cluster) but I was hoping the placement of a special WamI button in the cluster report meant I could get an overall report of all the clusters instead of having to click through them all individually.

Can you correct these assumptions, if they need correcting? And if they don't, can you advise anything else to diagnose what's happening? I'm using the most recent AFNI.

Thanks very much,

Shane