The AFNI TTatlas+tlrc Dataset
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The purpose of this Web page is to describe the format of the TTatlas+tlrc dataset and some files extracted from it (using 3dmaskdump and sed).
The dataset itself can be downloaded from these two files:
To be used from within AFNI, these files should be placed in the directory with the AFNI executables and plugins.-- RW Cox - 23 Mar 2003
Area and Gyral locations extracted from the TTatlas+tlrc Dataset
I have extracted the "area" and "gyral" regions from the dataset and stored them in two files:
- TTareas.txt.gz [1.2 MB compressed]
- TTgyral.txt.gz [3.0 MB compressed]
gzip -dv TT*.txt.gzwhich will leave you with files TTareas.txt and TTgyral.txt. Each file will uncompress to be about 10 times larger than its ".gz" version.
Each 1x1x1 mm3 voxel that has a nonzero label gets one line in each file. The following are some lines extracted from the TTareas.txt file:
-26 2 -22 AmygdalaThe 3 numbers are the (x,y,z) coordinates of the voxel, in the AFNI 'RAI' order:
-25 2 -22 Amygdala
-24 2 -22 Amygdala
-23 2 -22 Amygdala
-22 2 -22 Amygdala
-29 10 -22 Hippocampus
-28 10 -22 Hippocampus
-x = Right +x = LeftThe origin of coordinates is the Anterior Commissure (of course). To convert coordinates to the 'LPI' order used by SPM, change the signs of the (x,y) values (but not the z value!).
-y = Anterior +y = Posterior
-z = Inferior +z = Superior
To extract all the "Hippocampus" lines to file Hip.txt, the following Unix command should work:
grep Hippocampus TTareas.txt > Hip.txtThe complete list of area and gyral names is given in the dataset description below. In these TT*.txt files, the blanks in the region names have been replaced by the underscore "_" character, to make it easy to read the lines into a program (e.g., in C, one could use a format "%f%f%f%s" to read each line into 3 floats and a char array).
Format of TTatlas+tlrc Dataset
The dataset that provides the Talairach Daemon database for AFNI is stored in a dataset named TTatlas+tlrc. This dataset has 2 byte-valued sub-bricks at 1 mm resolution (please note that it is stored at the "small Talairach brick" size). Sub-brick #0 contains the "gyral" information; sub-brick #1 contains the "area" information. (These corresponded to database "levels" 3 and 5 in the original database from San Antonio. The other levels were at a much cruder level, and have been discarded in AFNI.)
Two sub-bricks are needed because some voxels have more than one label. In fact, there are more than 255 gyral/area combinations present in the database, so it is impossible to store the database in 1 byte/voxel.
The TTatlas+tlrc regions look fairly crude in the I-S direction because they are based on the Axial plates from the Atlas. In the gaps (up to 5Â mm), values from the database were propagated vertically to fill in the holes of the original database, much as the Talairach Daemon does when queried online.
The values stored in a voxel determine what it has been labeled as in the Talairach-Tournoux Atlas. These values are given in the table below, in the order they appear in the AFNI menus. AÂ value of 0 means that the voxel is not labeled. (Values not shown here represent the cruder gradations in the original database that were discarded; for example, Gray Matter was 79 and White Matter was 80.)
The AFNI TTatlas+tlrc Dataset
Sub-brick # Value Structure Name 1 68 Hippocampus 1 71 Amygdala 0 20 Posterior Cingulate 0 21 Anterior Cingulate 0 22 Subcallosal Gyrus 0 24 Transverse Temporal Gyrus 0 25 Uncus 0 26 Rectal Gyrus 0 27 Fusiform Gyrus 0 28 Inferior Occipital Gyrus 0 29 Inferior Temporal Gyrus 0 30 Insula 0 31 Parahippocampal Gyrus 0 32 Lingual Gyrus 0 33 Middle Occipital Gyrus 0 34 Orbital Gyrus 0 35 Middle Temporal Gyrus 0 36 Superior Temporal Gyrus 0 37 Superior Occipital Gyrus 0 39 Inferior Frontal Gyrus 0 40 Cuneus 0 41 Angular Gyrus 0 42 Supramarginal Gyrus 0 43 Cingulate Gyrus 0 44 Inferior Parietal Lobule 0 45 Precuneus 0 46 Superior Parietal Lobule 0 47 Middle Frontal Gyrus 0 48 Paracentral Lobule 0 49 Postcentral Gyrus 0 50 Precentral Gyrus 0 51 Superior Frontal Gyrus 0 52 Medial Frontal Gyrus 0 70 Lentiform Nucleus 1 72 Hypothalamus 1 73 Red Nucleus 1 74 Substantia Nigra 0 75 Claustrum 0 76 Thalamus 0 77 Caudate 1 124 Caudate Tail 1 125 Caudate Body 1 126 Caudate Head 1 128 Ventral Anterior Nucleus 1 129 Ventral Posterior Medial Nucleus 1 130 Ventral Posterior Lateral Nucleus 1 131 Medial Dorsal Nucleus 1 132 Lateral Dorsal Nucleus 1 133 Pulvinar 1 134 Lateral Posterior Nucleus 1 135 Ventral Lateral Nucleus 1 136 Midline Nucleus 1 137 Anterior Nucleus 1 138 Mammillary Body 1 144 Medial Globus Pallidus 1 145 Lateral Globus Pallidus 1 151 Putamen 1 146 Nucleus Accumbens 1 147 Medial Geniculum Body 1 148 Lateral Geniculum Body 1 149 Subthalamic Nucleus 1 81 Brodmann area 1 1 82 Brodmann area 2 1 83 Brodmann area 3 1 84 Brodmann area 4 1 85 Brodmann area 5 1 86 Brodmann area 6 1 87 Brodmann area 7 1 88 Brodmann area 8 1 89 Brodmann area 9 1 90 Brodmann area 10 1 91 Brodmann area 11 1 93 Brodmann area 13 1 94 Brodmann area 17 1 95 Brodmann area 18 1 96 Brodmann area 19 1 97 Brodmann area 20 1 98 Brodmann area 21 1 99 Brodmann area 22 1 100 Brodmann area 23 1 101 Brodmann area 24 1 102 Brodmann area 25 1 103 Brodmann area 27 1 104 Brodmann area 28 1 105 Brodmann area 29 1 106 Brodmann area 30 1 107 Brodmann area 31 1 108 Brodmann area 32 1 109 Brodmann area 33 1 110 Brodmann area 34 1 111 Brodmann area 35 1 112 Brodmann area 36 1 113 Brodmann area 37 1 114 Brodmann area 38 1 115 Brodmann area 39 1 116 Brodmann area 40 1 117 Brodmann area 41 1 118 Brodmann area 42 1 119 Brodmann area 43 1 120 Brodmann area 44 1 121 Brodmann area 45 1 122 Brodmann area 46 1 123 Brodmann area 47 0 53 Uvula of Vermis 0 54 Pyramis of Vermis 0 55 Tuber of Vermis 0 56 Declive of Vermis 0 57 Culmen of Vermis 0 58 Cerebellar Tonsil 0 59 Inferior Semi-Lunar Lobule 0 60 Fastigium 0 61 Nodule 0 62 Uvula 0 63 Pyramis 0 66 Culmen 0 65 Declive 1 127 Dentate 0 64 Tuber 0 67 Cerebellar Lingual
