Oxford Centre for Computational Neuroscience
Professor Edmund T Rolls
Automated Anatomical Labelling Atlas 3, AAL3
Following a first version AAL of the automated anatomical labeling atlas (Tzourio-Mazoyer et al., 2002), a second version (AAL2) (Rolls, Joliot, & Tzourio-Mazoyer, 2015) was developed that provided an alternative parcellation of the orbitofrontal cortex. We now provide a third version, AAL3 (Rolls, Huang, Lin, Feng and Joliot (2019)), which adds a number of brain areas not previously defined, but of interest in many neuroimaging investigations. The 26 new areas in the third version are subdivision of the anterior cingulate cortex into subgenual, pregenual and supracallosal parts; subdivision of the thalamus into 15 parts; the nucleus accumbens, substantia nigra, ventral tegmental area, red nucleus, locus coeruleus, and raphe nuclei. The new atlas is available as a toolbox for SPM, and can be used with MRIcron.
The automated anatomical atlas 3, AAL3, is a parcellation of the spatially normalized single-subject high- resolution T1 volume provided by the Montreal Neurological Institute (MNI). This includes the original parcellation provided in AAL (Tzourio-Mazoyer et al., 2002), the new parcellation of the orbitofrontal cortex provided in AAL2 (Rolls et al., 2015), but also new areas, as described in this User Guide and by Rolls, Huang, Lin, Feng and Joliot (2019).
AAL3, released on the 27 August 2019:
SPM12 version of AAL3 software: AAL3_for_SPM12.tar.gz
As in the previous realeases of AAL, AAL3 is provided with isotropic voxel size 2x2x2 mm. In addition, AAL3_1mm is also provided with a 1x1x1 mm voxel sampling size. Note that only the AAL3 added regions benefit from this finer spatial definition.
1) Copy the archive to the chosen location (e.g. /usr/local/soft/spm12/toolbox) unix> cp AAL3_for_SPM12.tar.gz /usr/local/soft/spm12/toolbox
unix> cd /usr/local/soft/spm12/toolbox
2) Gunzip and untar the archive will create an aal directory unix> tar -zxvf AAL3_for_SPM12.tar.gz
3) Add this directory to your Matlab path and copy the 4 files in your SPM12/atlas directory: unix> mkdir /usr/local/soft/spm12/atlas
unix> cp /usr/local/soft/spm12/toolbox/aal3/AAL3.nii /usr/local/soft/spm12/atlas unix> cp /usr/local/soft/spm12/toolbox/aal3/AAL3.xml /usr/local/soft/spm12/atlas unix> cp /usr/local/soft/spm12/toolbox/aal3/AAL3_1mm.nii /usr/local/soft/spm12/atlas
unix> cp /usr/local/soft/spm12/toolbox/aal3/AAL3_1mm.xml /usr/local/soft/spm12/atlas
4) To install AAL3 for mricron software:
unix> cp /usr/local/soft/spm12/toolbox/aal3/AAL3.nii.gz /usr/local/soft/mricron/templates unix> cp /usr/local/soft/spm12/toolbox/aal3/AAL3.nii.txt /usr/local/soft/mricron/templates unix> cp /usr/local/soft/spm12/toolbox/aal3/AAL3_1mm.nii.gz /usr/local/soft/mricron/templates
unix> cp /usr/local/soft/spm12/toolbox/aal3/AAL3_1mm.nii.txt /usr/local/soft/mricron/templates
(In Windows, copy the 4 files AAL3.nii.gz, AAL3.nii.txt and AAL3_1mm.nii.gz and AAL3_1mm.nii.txt into mricron/templates.)
1) Launch Matlab unix> matlab
2) First option: launch AAL3 from SPM12:
>> spm fmri
Select the desired contrast, mask, probability and extent threshold like in the regular spm_result. In the SPM12 Menu window:
Toolbox / AAL3
Then choose a labeling procedure as below from the instructions (4).
3) An alternative is to launch AAL from the Matlab command window:
Select the desired contrast, mask, probability and extent threshold like in the regular spm_result. Then choose a labeling procedure as below from the instructions (4).
4) Choose a labeling procedure. The 3 choices are explained and documented in the paper (Tzourio-Mazoyer et al., 2002):
· Local maxima labeling
· Extended local maxima labeling
· Cluster labeling
5) For "Extended local maxima labeling" input the local maxima radius of the sphere in millimeters (default 10 mm).
6) Select the anatomical parcellation database In /usr/local/soft/spm12/toolbox/AAL3
The file: ROI_MNI_V6.nii (2mm voxel edge, same file than AAL3) or
The file: ROI_MNI_V6_1mm.nii (1mm voxel edge, same file than AAL3_1mm)
7) There is also a third option to get the label:
>> spm fmri
Select the desired contrast, mask, probability and extent threshold like in the regular spm_result. In the SPM12 Results window: Atlas / Label using / AAL3
Then you get the label with a right click on the coordinates in the Graphic window.
Rolls, E. T., Huang, C. C., Lin, C.-P., Feng, J., & Joliot, M. (2019). Automated anatomical labelling atlas 3. Neuroimage, in revision.
Rolls, E. T., Joliot, M., & Tzourio-Mazoyer, N. (2015). Implementation of a new parcellation of the orbitofrontal cortex in the automated anatomical labeling atlas. Neuroimage, 122, 1-5. doi: 10.1016/j.neuroimage.2015.07.075
Tzourio-Mazoyer, N., Landeau, B., Papathanassiou, D., Crivello, F., Etard, O., Delcroix, N., . . . Joliot, M. (2002). Automated anatomical labeling of activations in SPM using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. Neuroimage, 15(1), 273-289. doi: 10.1006/nimg.2001.0978