Announcing the release of AFNI's adaptation of Eickhoff's Anatomy Toolbox.

The atlases used in the Anatomy Toolbox (see Eickhoff et al. Neuroimage 25 (2005), http://www.fz-juelich.de/ime/spm_anatomy_toolbox) has been generously provided to us by Drs Amnunts, Eickhoff and Zilles from 'Institut for Medicine (IME) Research Center Julich, Germany'. The atlases have been transformed to TLRC space for internal consistency within AFNI but coordinates are reported in TLRC, MNI and MNI Anatomical spaces. As in the Anatomy Toolbox, the atlases are in alignment with the N27 template.

Uses and New Features:
   ++ 'whereami': Both interactive and command-line versions will report findings from the TT_Daemon atlas (courtesy of Drs. Jack Lancaster and Peter Fox of RIC UTHSCSA) and the Cytoarchitectonic and Macro-Labels atlases provided in the Anatomy Toolbox. Here is a sample report from whereami:
   
         +++++++ nearby Atlas structures +++++++

         Focus point (LPI)=
             -21 mm [L], -17 mm [P],  55 mm [S] {T-T Atlas}
             -21 mm [L], -20 mm [P],  59 mm [S] {MNI Brain}
             -23 mm [L],  -9 mm [P],  65 mm [S] {MNI Anat.}

         Atlas TT_Daemon: Talairach-Tournoux Atlas
            Within 1 mm: Left  Precentral Gyrus
            Within 3 mm: Left  Middle Frontal Gyrus
                   -AND- Left  Brodmann area 6
            Within 6 mm: Left  Brodmann area 4
            Within 7 mm: Left  Postcentral Gyrus
                   -AND- Left  Medial Frontal Gyrus

         Atlas CA_N27_MPM: Cytoarch. Max. Prob. Maps (N27)
            Focus point: Area 6

         Atlas CA_N27_ML: Macro Labels (N27)
            Focus point: Left Precentral Gyrus
            Within 1 mm: Left Superior Frontal Gyrus
            Within 5 mm: Left Paracentral Lobule
            Within 6 mm: Left SMA
            Within 7 mm: Left Middle Frontal Gyrus

         Atlas CA_N27_PM: Cytoarch. Probabilistic Maps (N27)
            Focus point: Area 6   (p = 0.50)

         Atlas CA_N27_LR: Left/Right (N27)
            Focus point: Right Brain

   
   The command-line version of 'whereami' has been extensively modified, the program now does a lot more than it used to. Check it out. 
   
   ++ ROI selection with symbolic notaion: You can now specify ROIs using symbolic notation. For example, CA_N27_ML:left:hippo specifies the left
hippocampus in the CA_N27_ML atlas. This symbolic notation can be used to create masks on the fly. For example: 3dcalc -a 'CA_N27_ML::hippo' ... would automatically load into variable 'a' a mask of the bilateral hippocampus, according the the Macro Labels atlas dataset.
   
   ++ New ROI colormaps: New color maps (colorscales), optimized for use with ROIs, are now provided in AFNI. These color maps are accessible by:
       o setting the color map number chooser to '**' 
       o right-clicking on the color map and selecting 'Choose Colorscale'
       o picking one of: CytoArch_ROI_256, CytoArch_ROI_256_gap, ROI_32. etc.
       o setting autorange off and setting the range to the number of colors in the chosen map (256, 32, etc.). Color maps CytoArch_ROI_256_gap was created for the proper viewing of the Maximum Probability Maps of the Anatomy Toolbox.

The Download:
   You will need AFNI's very latest version (post Feb. 14, 2006).
   ++ TT-Daemon (a pre-requisite):
      http://afni.nimh.nih.gov/pub/dist/tgz/TTatlas+tlrc.HEAD
      http://afni.nimh.nih.gov/pub/dist/tgz/TTatlas+tlrc.HEAD
   ++ Anatomy Toolbox (version 1.3b):
      http://afni.nimh.nih.gov/pub/dist/tgz/CA_EZ_v1.3b.tgz  
   NOTE: See whereami -help for information on where to put the TT-Daemon and Anatomy Toolbox data. The easiest is to copy them into AFNI's binaries directory. 
   ++ N27 surface models:
      http://afni.nimh.nih.gov/pub/dist/tgz/suma_tlrc.tgz
   

WARNING:
   ++ There have been errors in the databases and perhaps the query functions. 
   Only fools expect none to occur in the future. Be wise.
         
NOTICE:
   ++ When using the Anatomy Toolbox atlases, please reference the proper publications and abide by the notice provided in the output of 'whereami -help' under the section 'Anatomy Toolbox Reference and Warning'. 

cheers,
Ziad for SSCC