afni.nimh.nih.gov

Dear Colleagues,

Hi. I have a problem with the "Go to atlas location" AFNI feature. Please correct any statements that are misunderstandings along the way.

At first, I had no environment variables set. I would use
TT_N27_SSW.nii.gz
as my underlay and
TT_N27_EZ_ML+tlrc.*
as my overlay. Fun. Great. If I wanted to use "Go to atlas location," I could use the default TT_Daemon to roughly go somewhere, and it worked.

I then learned that
TT_N27_EZ_ML+tlrc.*
is sort of depreciated. Logical because it is not listed anywhere in this
AFNI_atlas_spaces.niml
file. I should instead use this
TT_caez_ml_18+tlrc.*
dataset. I say sort of because the macrolabels are the same (https://afni.nimh.nih.gov/afni/community/board/read.php?1,156152,156167#msg-156167). My first problem was I still needed to use the depreciated file because the macrolabels would not appear in AFNI when clicking on the region. This
(base) picchionid@raid ~> 3dinfo -labeltable /misc/prog/afni/current.x86_64/TT_caez_ml_18+tlrc.HEAD
NO_LABEL_TABLE
is consistent with that potential problem.

I then added
AFNI_ATLAS_LIST = CA_N27_ML
AFNI_ATLAS_COLORS = CA_N27_ML
to my .afnirc file because in
AFNI_atlas_spaces.niml
CA_N27_ML is the atlas name for that dataset. Now I use
TT_caez_ml_18+tlrc.*
as the overlay. This solved the problem where macrolabels would not appear in AFNI when clicking on the region. However, when I now try to use "Go to atlas location," all the coordinates are 0, 0, 0 as show in the attached screenshot. What happened?

Sincerely,

Dante