AFNI Atlas Update

The close of 2023 brings a lot of changes to the default atlases and templates in a standard AFNI distribution. Here is a list of the major changes to the data and AFNI source code with some details below:

  1. New atlases added.
  2. Old atlases and templates removed.
  3. Default for "Show atlas colors" and "Go to atlas location" now connected to regions from the new Brodmann_Pijn_AFNI atlas.
  4. MNI spaces in templates and atlases specify the version of MNI template space like MNI_N27 or MNI_2009c_asym.
  5. Default search list of atlases that whereami uses includes a subset of the "modern" set.
  6. Default spaces shown in whereami are MNI and TLRC. MNI_ANAT is removed.
  7. AFNI history notes in the AFNI header and the label field in the NIFTI header include version and short description of atlases.

New atlases:
Brodmann atlases - the classic Brodmann_Pijn (MNI_N27) and Brodmann_Pijn_AFNI (MNI_2009c) atlases redrawn. These were made available courtesy of Martjin van Heuvel. The AFNI version in MNI_2009c is reprojected into the 2009c template and regularized with modal smoothing. There will be a further announcement with some more description.

JulichBrain atlases - Julich_MNI2009c and Julich_MNI_N27 largely replace the previous MPM (maximum probability map) atlases from the older cytoarchitectonic atlases from Eickhoff-Zilles. These have many more regions than the previous CA_MPM 1.8 and 2.2 versions. We expect to see these atlases to get updated regularly (

Freesurfer atlases - Generated Desikan-Killiany parcellations based on recon-all for the TT_N27 and MNI_2009c templates.

Removed atlases and templates:
TTatlas - the Talairach daemon atlas is gone with its many inherent errors and limitations.
CA_MPM_18 - older 1.8 version is removed, and slightly newer 2.2 version is kept for now.

All MNI_ANAT atlases are removed to avoid confusion.

The original MNI_152 and ICBM_452 templates for T1, T2 and EPI - these relatively blurry, low resolution (2mm) MNI templates are some of the oldest templates for MRI use, but they have long seen little use with modern nonlinear alignment and flexible cost functions. The Talairached variants of these templates are also removed.

Several atlases were removed from standard distribution but may still be useful for select purposes. The Vm_PFC atlas for the ventromedial prefrontal cortex, the TT_dd_desai_mpm and the TT_dk_desai_mpm atlases will continue to be available on our website.

All removed templates and atlases will continue to be downloadable from the AFNI website.

AFNI commands and environment variables:
To see the current list of atlases included with afni:

   whereami -show_atlases

++ ----- Atlas list: -------
++ Name             Space    Dataset              Description
++ __________________________________________________________
++ MNI_Glasser_HCP_v1.0      MNI_2009c_asym  MNI_Glasser_HCP_v1.0.nii.gz Glasser HCP 2016 surface-based parcellation      
++ Brainnetome_1.0           MNI             BN_Atlas_246_1mm.nii.gz Brainnetome MPM                                      
++ CA_MPM_22_MNI             MNI             MNI_caez_mpm_22+tlrc Eickhoff-Zilles MPM atlas                                
++ CA_MPM_22_TT              TT_N27          TT_caez_mpm_22+tlrc Eickhoff-Zilles MPM atlas 2.2 - Talairach space          
++ CA_N27_ML                 TT_N27          TT_caez_ml_18+tlrc Macro Labels (N27)                                        
++ CA_N27_GW                 TT_N27          TT_caez_gw_18+tlrc Cytoarch. Prob. Maps for gray/white matter 1.8            
++ CA_ML_18_MNI              MNI_N27         MNI_caez_ml_18+tlrc Macro Labels (N27-MNI)                                      
++ CA_LR_18_MNI              MNI_N27         MNI_caez_lr_18+tlrc Left/Right (N27-MNI)                                        
++ Haskins_Pediatric_Nonline HaskinsPeds     HaskinsPeds_NL_atlas1.01+tlrc.HEAD Version 1.01                                                
++ FS.afni.MNI2009c_asym     MNI_2009c_asym  FS.afni.MNI2009c_asym.nii.gz Freesurfer MNI2009c DK parcellation                        
++ FS.afni.TTN27             TT_N27          FS.afni.TTN27.nii.gz Freesurfer TT_N27 DK parcellation                          
++ Brodmann_Pijn             MNI_N27         Brodmann.nii.gz Brodmann atlas MNI N27 - Pijnenburg                        
++ Brodmann_Pijn_AFNI        MNI_2009c_asym  Brodmann_pijn_afni.nii.gz Brodmann atlas for MNI 2009c - Pijnenburg AFNI version      
++ Julich_MNI2009c           MNI_2009c_asym  Julich_MNI2009c.nii.gz JulichBrain 3.0 for MNI 2009c asymmetric space              
++ Julich_MNI_N27            MNI_N27         Julich_MNI_N27.nii.gz JulichBrain 3.0 for MNI N27 space                          

Output also includes new citation information. Please cite the contributors of these atlases appropriately.

AFNI atlas environment variables:
These AFNI variables are typically set in the users ~/.afnirc file. They control whereami's behavior for atlas searching and locations:

AFNI_ATLAS_COLORS - sets default atlas to be used for the "Show atlas colors" and "Go to atlas location" in the afni GUI. It is now set effectively to default to Brodmann_Pijn_AFNI.

AFNI_ATLAS_LIST - default search list. This may be set to ALL or a comma separated list of the AFNI atlas names. By default, this is effectively set to Brodmann_Pijn_AFNI,MNI_Glasser_HCP_v1.0,

AFNI_TEMPLATE_SPACE_LIST - default list of spaces coordinates shown in the whereami output (GUI or command line). By default, this is set to "MNI,TLRC".

AFNI_SUPP_ATLAS_DIR - if adding other atlases, set this variable to point to the single directory with the atlases and the CustomAtlases.niml file describing the atlases.

Many of these changes are described in more detail in our recent Bootcamp class material here (starting at slide 24):

Please let us know if these changes are useful or if you run into any issues.