AAL3 User Guide
The automated anatomical parcellation AAL3 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, Joliot, and Tzourio-Mazoyer, 2015) , but also new
areas, as described in this User Guide and by (Rolls et al., 2019).
Download
AAL3, released on the 27 August 2019:
SPM12 version of AAL3 software: AAL3_for_SPM12.tar.gz
User guide
Following a first version AAL of the automated anatomical labeling atlas (Tzourio-Mazoyer et al
2002), a second version (AAL2) (Rolls, Joliot, and Tzourio-Mazoyer, 2015) was developed that
provided an alternative parcellation of the orbitofrontal cortex following the description provided
by Chiavaras, Petrides, and colleagues. We now provide a third version, AAL3, which adds a
number of brain areas not previously defined, but of interest in many neuroimaging investigations.
The new areas in the third version are subdivision of the anterior cingulate cortex into subgenual,
pregenual and supracallosal parts; the thalamus; 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.
As in the previous realease 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
the AAL3 added regions benefit from this finer spatial definition.
How to install the software
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
