Hello,
Hope you're all doing well! I have a simple question about the draw ROI plugin.
I'm interested in import some atlas regions as ROIs, and I'm interested in the Glasser HCP atlas. I learned that I can use whereami from the documentation, for example this is the command I tried:
$whereami -mask_atlas_region MNI_Glasser_HCP_v1.0:left:L_Primary_Visual_Cortex -prefix roi.lv1.mni

When I looked at the generated ROI in a subject's MNI warped anat (e.g., subj_anat_tlrc) volume, it looks about right, which is great. But I also saw the video where the interactive draw ROI plugin was used. So I loaded subj_anat_tlrc, then start the plugin, copy the dataset, then choose the same atlas, choose left primary visual cortex, click Load:overwrite. Now I get the pink ROI in the image, which is way off. I had assumed that the two methods (command line above) and this interactive way of doing things are equivalent, but apparently that's not the case. I'm probably doing something wrong here, but it's not obvious to me. Could you advise?

While on the same topic, I'm just curious, how does AFNI keep track of different template spaces? For example, while loading the same anat, I can apparently choose the TT_Daemon as the atlas, But I thought that one is in the Tailarach space. Does AFNI automatically perform spatial transformation if I load a region from TT_Daemon? Incidentally, I did try to load Boradmann area 17, and it is actually quite close (the purple region in the image). I don't understand--the Glasser atlas is supposed in the same space but it's way off, yet the TT_Daemon is in a different space, but it looks Ok.

Thank you very much.

Best,

--Taosheng