Hello! I recently updated my .afnirc file and added some atlases to my abin folder. Somehow in the process, whereami seems to have disappeared from the AFNI GUI. Now when I right click on a brain image, it says "bg =somenumber" where it used to let me click whereami. Also, when I load AFNI it gives me the warning "Can't find TTatlas+tlrc or TTatlas.nii.gz dataset for 'whereami'". However, I have TTatlas+tlrc.HEAD and TTatlas+tlrc.BRIK.gz files in my abin folder. Do you have any suggestions for how I can get whereami back into my GUI? Thanks!
AFNI stopped including that particular atlas last year, but you should still be able to get a whereami interface to show up with the other atlases. The atlases are distributed on our website and through our install scripts. Besides the atlas datasets, there should also be the AFNI_atlas_spaces.niml file that describes which atlases and spaces exist. By default, these usually go in the same directory as the AFNI binaries, but you can put them elsewhere and define the AFNI_ATLAS_PATH to point to it. Make sure you have a recent version of AFNI, and check for the existence of the that file and the atlas datasets that go with it.
https://afni.nimh.nih.gov/pub/dist/atlases/afni_atlases_dist.tgz
Seems like updating the binaries was sufficient, thank you!
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Note that due to conflict with a program that exists elsewhere on Linux, AFNI's beloved whereami actually had to be renamed to whereami_afni. For a while we are continuing to distribute both, but eventually we will only use the latter.
Also, regarding the TTatlas dataset, it should never really be used in an ROI-based analysis. I believe it was translated from a paper atlas long ago, and given to us to distribute as a translation of that. It might be possibly considered usable for getting approximate location, but it should not be used for quantitative work. To give a flavor of this, it looks like this on the TT_N27 template:
There are much more modern atlases for getting either location or regions of interest. This is what the FreeSurfer atlas in TT_N27 space (FS.afni.TTN27.nii.gz) looks like, for comparison:
--pt