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AAL2

Original article

Implementation of a new parcellation of the orbitofrontal cortex in the automated anatomical labeling atlas.
Rolls ET, Joliot M & Tzourio-Mazoyer N (2015) . NeuroImage 10.1016/j.neuroimage.2015.07.075. (PDF)

Download

AAL2 for SPM12: aal2_for_SPM12.tar.gz

Overview

An alternative parcellation of the orbitofrontal cortex is described for the automated anatomical labeling atlas of Tzourio-Mazoyer et al. (2002) (Automated anatomical labeling of activations in SPM using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. NeuroImage 15:273-289). The new parcellation of the orbitofrontal cortex follows the description provided by Chiavaras, Petrides, and colleagues (2000, 2001).

Figure: Frontal lobe inferior surface, identification of sulci (A) that were used to parcellate using axial slices from -10 to -24 the new orbitofrontal regions in AAL2 corresponding to the Medial, Anterior, Posterior and Lateral orbital gyri (B).

How to install the software

1) Copy the archive to the chosen location (e.g. /usr/local/soft/spm12/toolbox)
unix> cp aal2_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 aal2_for_SPM12.tar.gz

3) Add this directory to your Matlab path and copy 2 files in your SPM12/atlas directory
unix> setenv MATLABPATH $MATLABPATH:/usr/local/soft/spm12/toolbox/aal
unix> cp /usr/local/soft/spm12/toolbox/aal/AAL2.nii /usr/local/soft/spm12/atlas
unix> cp /usr/local/soft/spm12/toolbox/aal/AAL2.xml /usr/local/soft/spm12/atlas

To install AAL2 in mricron software:
unix> cp /usr/local/soft/spm12/toolbox/aal/aal2.nii.gz /usr/local/soft/mricron/templates
unix> cp /usr/local/soft/spm12/toolbox/aal/aal2.nii.lut /usr/local/soft/mricron/templates
unix> cp /usr/local/soft/spm12/toolbox/aal/aal2.nii.txt /usr/local/soft/mricron/templates

How to use the software

1) Launch Matlab
unix> matlab

2) First option: launch AAL 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 / aal
Then choose a labeling procedure as below from the instructions 3).

2bis) An alternative is to launch AAL from the Matlab command window:
>> aal
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 3).

3) Choose a labeling procedure. The 3 choices are explained and documented in
the NeuroImage paper (Tzourio-Mazoyer et al., 2002):

  • Local maxima labeling
  • Extended local maxima labeling
  • Cluster labeling

4) For "Extended local maxima labeling" input the local maxima radius of the
sphere in millimeters (default 10 mm).

5) Select the anatomical parcellation database
In /usr/local/soft/spm12/toolbox/aal
The file: ROI_MNI_V5.img

_

There is also a third option to get the label:
unix> matlab
>> 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 / AAL2
Then you get the label with a right click on the coordinates in the Graphic window.

Note

If the "unknown" label appears, it might be that the local maximum is at the edge of the template.
Then, move your cursor on the label to display the proportion of the voxels in the surrouding ROIs. See below as an example.


Any question?

Please contact us by email at: aal2.gin.brainatlas at gmail.com

Date: 27th of August, 2015