We are trying to create some refined ROIs for further analyses. The regions of interest do not map on very well to the ready-made masks in the afni plug-ins. I know one solution is to draw the ROIs yourself, but we were hoping to use something more standardized. I had 2 questions in this regard:

1) Is it possible to download additional anat ROI libraries (e.g., Pick Atlas) that would work in the plugin? For example, entering the whereami command yields output from a number of atlases. Can these be made available in the plug-ins/drawdataset function to draw alternative ROIs?

2) Related to that, I am trying to use an anatomical mask derived from pickatlas and import it into something that I can use with Afni. I used the 3dcopy command, but I am having all kinds of trouble when I try to treat it as I would an anatomical mask or functional mask generated through the usual route (drawdataset or a functional ROI using 3dmerge).

I've attached some sample ROIs. The command I'm using is:

3dcopy l_amyg_1_aal.hdr pickroi_lamyg1_aal

I will try to upload the Analyze files separately (.hdr and .img).

I end up with a file that is not visible when paired with an anat file or appears in the wrong orientation (flipped L-R or Anterior-posterior depending on the workstation).

Is there a simple way to interface Analyze format masks for use with afni?

Thanks so much,
Derek.