Anatomical Automatic Labeling (AAL) For SPM8 Version v1 Date 14/06/2010 E-mail : aalgin@cyceron.fr. Anatomical Automatic Labeling (AAL) is a package for the anatomical labeling of functional brain mapping experiments. It is an in-house package made by Neurofonctional Imaging Group (GIN, UMR6232, CYCERON, Caen ,France), which is available to the scientific community as a copyright freeware under the terms of the GNU General Public Licence. I Goal II Reference III Distribution IV How to install the software V How to use the software VI Bibliography VII Contact VIII History I Goal This project has been initiated in the nineties with the construction of a set of rules to be used for the anatomical parcellation of the brain according to major sulci and gyri. We applied this set of rules to built an anatomical parcellation of the spatially normalized single subject high resolution T1 volume provided by the Montreal Neurological Institute (MNI) (Collins et al., 1998). The MNI single subject main sulci were first delineated and further used as landmarks for the 3D definition of 45 Anatomical Volumes Of Interest (AVOI) in each hemisphere. This procedure was performed using a dedicated software which allowed a 3D following of the sulci course on the edited brain. Regions of interest were then drawn manually using the same software every 2 mm on the axial slices of the high resolution MNI single subject. The 90 AVOI were reconstructed and assigned a label. Using this parcellation method, three procedures to perform the automated anatomical labelling of functional studies are proposed : 1) labelling of an extremum defined by a set of coordinates, 2) percentage of voxels belonging to each of the AVOI intersected by a sphere centered by an extremum, 3) percentage of voxels belonging to each of the AVOI intersected by an activated cluster. An interface with the Statistical Parametric Mapping (SPM8) package (Friston et al., 1995) is provided as a freeware to researchers of the neuroimaging community. We believe that this tool is an improvement for the macroscopical labelling of activated area as compared to labelling assessed using the Talairach atlas brain in which deformations are well known. However, this tool does not alleviate the need for more sophisticated labelling strategies based on anatomical or cytoarchitectonic probabilistic maps. II Reference If you need to reference this work, please used the following reference : Tzourio-Mazoyer N, Landeau B, Papathanassiou D, Crivello F, Etard O, Delcroix N, et al. Automated anatomical labelling of activations in spm using a macroscopic anatomical parcellation of the MNI MRI single subject brain. Neuroimage 2002; 15: 273-289. III Distribution The distribution includes a readme.txt (this file), 4 parcellation definition files (the ROI_MNI_V4* files), and 9 program file (*.m files). III.1 ROI_MNI_V4.img (flat short integer image) and ROI_MNI_V4.hdr (header file in ANALYZE-7 format with slight customizations to the header as described in SPM help/spm_format.man and in Neurological Orientation (R is R)). Each anatomical region is associated a gray level (see III.2). Note that aal programs manage the orientation of your own analyze image (see defaults.analyze.flip variable). III.2 ROI_MNI_V4_list.mat : Matlab format file giving the correspondence between the anatomical region name and the gray level information. Anatomical-region-name(*) Gray-level Precentral_L 2001 Precentral_R 2002 Frontal_Sup_L 2101 Frontal_Sup_R 2102 Frontal_Sup_Orb_L 2111 Frontal_Sup_Orb_R 2112 Frontal_Mid_L 2201 Frontal_Mid_R 2202 Frontal_Mid_Orb_L 2211 Frontal_Mid_Orb_R 2212 Frontal_Inf_Oper_L 2301 Frontal_Inf_Oper_R 2302 Frontal_Inf_Tri_L 2311 Frontal_Inf_Tri_R 2312 Frontal_Inf_Orb_L 2321 Frontal_Inf_Orb_R 2322 Rolandic_Oper_L 2331 Rolandic_Oper_R 2332 Supp_Motor_Area_L 2401 Supp_Motor_Area_R 2402 Olfactory_L 2501 Olfactory_R 2502 Frontal_Sup_Medial_L 2601 Frontal_Sup_Medial_R 2602 Frontal_Med_Orb_L 2611 Frontal_Med_Orb_R 2612 Rectus_L 2701 Rectus_R 2702 Insula_L 3001 Insula_R 3002 Cingulum_Ant_L 4001 Cingulum_Ant_R 4002 Cingulum_Mid_L 4011 Cingulum_Mid_R 4012 Cingulum_Post_L 4021 Cingulum_Post_R 4022 Hippocampus_L 4101 Hippocampus_R 4102 ParaHippocampal_L 4111 ParaHippocampal_R 4112 Amygdala_L 4201 Amygdala_R 4202 Calcarine_L 5001 Calcarine_R 5002 Cuneus_L 5011 Cuneus_R 5012 Lingual_L 5021 Lingual_R 5022 Occipital_Sup_L 5101 Occipital_Sup_R 5102 Occipital_Mid_L 5201 Occipital_Mid_R 5202 Occipital_Inf_L 5301 Occipital_Inf_R 5302 Fusiform_L 5401 Fusiform_R 5402 Postcentral_L 6001 Postcentral_R 6002 Parietal_Sup_L 6101 Parietal_Sup_R 6102 Parietal_Inf_L 6201 Parietal_Inf_R 6202 SupraMarginal_L 6211 SupraMarginal_R 6212 Angular_L 6221 Angular_R 6222 Precuneus_L 6301 Precuneus_R 6302 Paracentral_Lobule_L 6401 Paracentral_Lobule_R 6402 Caudate_L 7001 Caudate_R 7002 Putamen_L 7011 Putamen_R 7012 Pallidum_L 7021 Pallidum_R 7022 Thalamus_L 7101 Thalamus_R 7102 Heschl_L 8101 Heschl_R 8102 Temporal_Sup_L 8111 Temporal_Sup_R 8112 Temporal_Pole_Sup_L 8121 Temporal_Pole_Sup_R 8122 Temporal_Mid_L 8201 Temporal_Mid_R 8202 Temporal_Pole_Mid_L 8211 Temporal_Pole_Mid_R 8212 Temporal_Inf_L 8301 Temporal_Inf_R 8302 Cerebelum_Crus1_L 9001 Cerebelum_Crus1_R 9002 Cerebelum_Crus2_L 9011 Cerebelum_Crus2_R 9012 Cerebelum_3_L 9021 Cerebelum_3_R 9022 Cerebelum_4_5_L 9031 Cerebelum_4_5_R 9032 Cerebelum_6_L 9041 Cerebelum_6_R 9042 Cerebelum_7b_L 9051 Cerebelum_7b_R 9052 Cerebelum_8_L 9061 Cerebelum_8_R 9062 Cerebelum_9_L 9071 Cerebelum_9_R 9072 Cerebelum_10_L 9081 Cerebelum_10_R 9082 Vermis_1_2 9100 Vermis_3 9110 Vermis_4_5 9120 Vermis_6 9130 Vermis_7 9140 Vermis_8 9150 Vermis_9 9160 Vermis_10 9170 (*) Note that the cerebral AVOI definitions are fully described in the paper by Tzourio-Mazoyer et al. (Tzourio-Mazoyer et al., 2002). The cerebellar AVOI definitions are based on the cerebellum parcellation proposed by Schmahmann et al. (Schmahmann et al., 1999). III.3 ROI_MNI_V4_Border.mat : Matlab format file listing the border of each region. This file is used in the automatic labeling procedure. III.4 the matlab program files : aal.m gin_clusters.m gin_clusters_plabels.m gin_det_dlabels.m gin_det_plabels.m gin_dlabels.m gin_list_dlabels.m gin_list_plabels.m gin_rclusters.m IV How to install the software. Note that aal procedures have been tested only on unix machines. IV.1 Copy the archive to the chosen location In this example we choose to install the software directly at the same location than the spm distribution (/usr/local/soft/spm8/toolbox) unix> cp aal_for_spm8.tar.Z /usr/local/soft/spm8/toolbox unix> cd /usr/local/soft/spm8/toolbox IV.2 Expand the archive will create an anat_aal_vb1 directory unix> uncompress aal_for_spm8.tar.Z unix> tar xvf aal_for_spm8.tar IV.3 Add this directory to your matlab path unix > setenv MATLABPATH ${MATLABPATH}:/usr/local/soft/spm8/toolbox/aal V How to use the software. V.1 Do a regular statistical analysis using spm8 V.2 Launch matlab unix > matlab V.3 launch aal >> aal V.4 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 V.5 Select the desired contrast, mask, probability and extent threshold like in the regular spm_result V.6 For "Extended local maxima labeling" input the local maxima radius of the sphere in millimeters (default 10 mm). V.7 Select the anatomical parcellation database : In /usr/local/soft/spm8/toolbox/aal The file ROI_MNI_V4.nii V.8 Results V.8.1 Local maxima labeling For each local maxima : -coordinates in mm x,y,z -anatomical label (see below) -distance in millimeter to this region. If the local maxima is inside a region this distance is null (0.00). If the local maxima is outside the parcellation the nearest region name is displayed in the previous column and the shortest distance from the local maxima to this region is listed (exp : 2.30 mm) -anatomical label of the local maxima to the second nearest region -shortest distance of the local maxima to the second nearest region -anatomical label of the local maxima to the third nearest region -shortest distance of the local maxima to the third nearest region V.8.2 Extended local maxima labeling Each local maxima is supposed to be a 10 mm (if the default is used) spherical region. The intersection of this volume and the AVOI is computed and the result sorted in a descending order according the percentage of overlap (exp : a result of Postcentral_L 100 % indicates that the 10mm radius region surrouding the local maxima is fully included in the Postcentral_L region) For each local maxima : -coordinates in mm x,y,z -list of anatomical label and percentage of overlap. Percentage less than 1% are not listed. If part of the region is outside the parcellation the anatomical label will list "OUTSIDE". V.8.3 Cluster labeling The intersection of each cluster and the AVOI is computed and the result sorted in a descending order according the percentage of overlap. For each local maxima : -coordinates in mm x,y,z of the most significative local maxima of the cluster -list of anatomical label and percentage of overlap. Percentage less than 1% are not listed. If part of the region is outside the parcellation the anatomical label will list "OUTSIDE". Example : a result of -44 -22 - 56 Postcentral_L 55.00 Precentral_L 31.00 OUTSIDE 10.00 Parietal_Sup_L 5.00 indicates that : 55% of the cluster volume is included in the Postcentral_L region 31% of the cluster volume is included in the Precentral_L region 10% of the cluster volume is outside the parcellation 5% of the cluster volume is included in the Parietal_Sup_L region VI Bibliography Collins DL, Zijdenbos AP, Kollokian V, Sled JG, Kabani NJ, Holmes CJ, et al. Design and construction of a realistic digital brain phantom. IEEE Transactions on Medical Imaging 1998; 17: 463-68. Friston KJ, Holmes AP, Worsley KJ, Poline JP, Frith CD, Frackowiak RSJ. Statistical parametric maps in functional imaging: A general linear approach. Human Brain Mapping 1995; 2: 189-210. Schmahmann JD, Doyon J, McDonald D, Holmes C, Lavoie K, Hurwitz AS, et al. Three-dimensional MRI atlas of the human cerebellum in proportional stereotaxic space. Neuroimage 1999; 10: 233-260. Tzourio-Mazoyer N, Landeau B, Papathanassiou D, Crivello F, Etard O, Delcroix N, et al. Automated anatomical labelling of activations in spm using a macroscopic anatomical parcellation of the MNI MRI single subject brain. Neuroimage 2002; 15: 273-289. VII Contact Any comments could be send to aalgin@cyceron.fr. VIII History Version v1 Date 14/06/2010 aal version for SPM8