Missing atlases in whereami

AFNI Message Board
1

Hi all,

a quick question. When using the “WhereAmI” button in the clusterize report window, I get the following warning messages in the terminal:

** Warning: Atlas CA_N27_PM could not be loaded.
** Warning: Atlas CA_PM_18_MNIA could not be loaded.
** Warning: Atlas DKD_Desai_PM could not be loaded.
** Warning: Atlas DD_Desai_PM could not be loaded.
** Warning: Atlas FS_Desai_PM could not be loaded.

I have actually re-downloaded the atlases tarball from:
https://afni.nimh.nih.gov/pub/dist/atlases/atlases_latest.tgz

and placed it in my ~/abin directory, but the warning remains because the corresponding atlases are still missing, as shown by “whereami -show_atlases”:

++ ----- Atlas list: -------
++ Name Space Dataset Description
++ __________________________________________________________
++ MNI_Glasser_HCP_v1.0 MNI /home/giuseppep/abin//MNI_Glasser_HCP_v1.0.nii.gz Glasser HCP 2016 surface-based parcellation
++ Brainnetome_1.0 MNI /home/giuseppep/abin//BN_Atlas_246_1mm.nii.gz Brainnetome MPM
++ CA_MPM_22_MNI MNI /home/giuseppep/abin//MNI_caez_mpm_22+tlrc Eickhoff-Zilles MPM atlas
++ CA_MPM_22_TT TT_N27 /home/giuseppep/abin//TT_caez_mpm_22+tlrc Eickhoff-Zilles MPM atlas 2.2 - Talairach space
++ CA_N27_ML TT_N27 /home/giuseppep/abin//TT_caez_ml_18+tlrc Macro Labels (N27)
++ CA_N27_MPM TT_N27 /home/giuseppep/abin//TT_caez_mpm_18+tlrc Cytoarch. Max. Prob. Maps
++ CA_N27_PM TT_N27 TT_caez_pmaps_18+tlrc Cytoarch. Probabilistic Maps 1.8
++ CA_N27_GW TT_N27 /home/giuseppep/abin//TT_caez_gw_18+tlrc Cytoarch. Prob. Maps for gray/white matter 1.8
++ CA_N27_LR TT_N27 /home/giuseppep/abin//TT_caez_lr_18+tlrc Left/Right (N27) 1.8
++ CA_ML_18_MNI MNI /home/giuseppep/abin//MNI_caez_ml_18+tlrc Macro Labels (N27-MNI)
++ CA_MPM_18_MNI MNI /home/giuseppep/abin//MNI_caez_mpm_18+tlrc Cytoarch. Max. Prob. Maps (MNI)
++ CA_LR_18_MNI MNI /home/giuseppep/abin//MNI_caez_lr_18+tlrc Left/Right (N27-MNI)
++ CA_ML_18_MNIA MNI_ANAT /home/giuseppep/abin//MNIa_caez_ml_18+tlrc Macro Labels (N27)
++ CA_MPM_18_MNIA MNI_ANAT /home/giuseppep/abin//MNIa_caez_mpm_18+tlrc Cytoarch. Max. Prob. Maps
++ CA_PM_18_MNIA MNI_ANAT MNIa_caez_pmaps_18+tlrc Cytoarch. Probabilistic Maps
++ CA_GW_18_MNIA MNI_ANAT /home/giuseppep/abin//MNIa_caez_gw_18+tlrc Cytoarch. Prob. Maps for gray/white matter
++ CA_LR_18_MNIA MNI_ANAT /home/giuseppep/abin//MNIa_caez_lr_18+tlrc Left/Right (N27)
++ DKD_Desai_PM TT_N27 TT_desai_dkpmaps+tlrc Probability maps of 35 cortical areas (gyri)
++ DD_Desai_PM TT_N27 TT_desai_ddpmaps+tlrc Probability maps of 75 cortical areas
++ FS_Desai_PM TT_N27 TT_desai_fspmaps+tlrc 40 subcortical areas
++ DD_Desai_MPM TT_N27 /home/giuseppep/abin//TT_desai_dd_mpm+tlrc Maximum probability maps of Desai DD and FS maps
++ DKD_Desai_MPM TT_N27 /home/giuseppep/abin//TT_desai_dk_mpm+tlrc Maximum probability maps of Desai DKD and FS maps
++ MNI_VmPFC MNI /home/giuseppep/abin//MNI_VmPFC+tlrc Ventromedial Prefrontal Cortex
++ TT_Daemon TLRC /home/giuseppep/abin//TTatlas+tlrc Talairach-Tournoux Atlas
++ Haskins_Pediatric_Nonline HaskinsPeds /home/giuseppep/abin//HaskinsPeds_NL_atlas1.0+tlrc.HEAD Version 1.0

My question is why are those atlases missing from the distribution? Is it because they are obsolete/superseded and somewhat the “whereami” function has not been notified?

thanks in advance for any comment/advice!
giuseppe

2

The probabilistic atlases were removed because they take up a lot of space, and most people do not seem to.use them. The atlases are defined in AFNI_atlas_spaces.niml if you did want to download the probabilistic maps (link provided below). The warnings from whereami are just warnings, so they could be ignored. I removed those particular warnings from whereami in the latest distribution.

https://afni.nimh.nih.gov/pub/dist/atlases/currentpmaps/

3

Hi Daniel,

thanks for your reply, I see. The sizes of the pmaps files are quite small though (a few mb), so it may be worthwhile to keep them in the distribution unless their usefulness/accuracy has not stood the test of time.

best
giuseppe

4

hi, Glen
Could I use probabilistic maps of Brodmann area Atlats by whereami in cluster reports? I am not sure how to add Brodmann area Atlats.