AAL Atlas

AAL Atlas

The AAL atlas (Automated Anatomical Labeling) can be used for CIVET. It is located at /project/m/mchakrav/quarantine/CIVET/1.1.12/build/Linux-x86_64/CIVET-1.1.12/models This AAL labeling package is specific to the resampled surfaces (163842/40962 vertices per hemisphere) generated from CIVET pipeline (Ad-Dab'bagh et al, Neuroimage, 2006). Note that the AAL template was originally defined on the MNI single brain (Colin27 brain, Tzourio-Mazoyer et al., 2002, Neuroimage) and registered to the ICBM surface model (Lyttelton et al., 2007, Neuroimage).

The package includes:

1. AAL_atlas_left.txt: 163842 labels for the ICBM surface model on left hemisphere
2. AAL_atlas_right.txt: 163842 labels for the ICBM surface model on right hemisphere
3. AAL_license.txt: reference and license agreement

Note that:

1. bilateral labels are different
2. the labelling number and regional name are consistent with the original reference (Tzourio-Mazoyer et al., 2002, Neuroimage).
3. the ICBM surface model refers to the surface after resampling (i.e. surface registration) to the averaged surface model (Lyttelton et al., 2007, Neuroimage).

Viewing the AAL Atlas

1. Copy the Color Map to ~/.config/MINC/textures/.
2. Locate a OBJ brain you can use, any brain with 40962 vertices (can be the Average brain you use in CIVET).
3. Locate the AAL_atlas_left and right TXT files.
4. Open in brain-view2

$ brain-view2 /path/to/average_left.obj /path/to/AAL_atlas_left.txt 

5. Choose the table in AAL_atlas_left, and choose the discrete.png from the color map. Arrange the range from 0 to 91 for correct viewing of the colors. You should be able to see this:

If you click on each label, you will see the label number in the Resources box.

Enjoy