Anatomical Automatic Labeling 2 (AAL2) for SPM12 E-mail: aal2.gin.brainatlas@gmail.com This archive provide an alternative parcellation of the orbitofrontal cortex for the automated anatomical labeling atlas of Tzourio-Mazoyer et al. (Tzourio-Mazoyer et al., 2002). The new parcellation of the orbitofrontal cortex follows the description provided by Chiavaras, Petrides, and colleagues (Chiavaras and Petrides, 2000; Chiavaras et al., 2001). The AAL2 atlas is described in the following publication: Rolls ET, Joliot M, Tzourio-Mazoyer N (2015) Implementation of a new parcellation of the orbitofrontal cortex in the automated anatomical labeling atlas. NeuroImage 10.1016/j.neuroimage.2015.07.075. Anatomical Automatic Labeling (AAL2) is a package for the anatomical labeling of functional brain mapping experiments. It is an in-house package made by the Neurofunctional Imaging Group (GIN, UMR5296, Bordeaux, France), which is available to the scientific community as copyright freeware under the terms of the GNU General Public License. The archive file aal2.tar.gz includes 2 sets of files: - The first set is to be used with the AAL software for SPM12 (provided through http://www.gin.cnrs.fr/AAL2) ROI_MNI_V5_vol.mat ROI_MNI_V5_List.mat ROI_MNI_V5_Border.mat ROI_MNI_V5_vol.txt ROI_MNI_V5.xml ROI_MNI_V5.nii AAL2.xml AAL2.nii - The second set is to be used with the mricron (http://www.mccauslandcenter.sc.edu/mricro/mricron) software: aal2.nii.gz aal2.nii.lut aal2.nii.txt Note 1: As shown in Table 2 of (Rolls, Joliot and Tzourio-Mazoyer 2015), eight new labels have been provided, OFCmed_L OFCmed_R OFCant_L OFCant_R OFCpost_L OFCpost_R OFClat_l OFClat_R Note 2: As shown in Table 2 of (Rolls, Joliot and Tzourio-Mazoyer 2015) six labels have been modified. This was chosen to emphasis that those regions, already present in the first version of aal (aal and ROI_MNI_V4), have been modified in the aal2 parcellation. Frontal_Sup_L changes to Frontal_Sup_2_L Frontal_Sup_R changes to Frontal_Sup_2_R Frontal_Mid_L changes to Frontal_Mid_2_L Frontal_Mid_R changes to Frontal_Mid_2_R Frontal_Inf_Orb_L changes to Frontal_Inf_Orb_2_L Frontal_Inf_Orb_R changes to Frontal_Inf_Orb_2_R Note 3: As shown in Table 2 of (Rolls, Joliot and Tzourio-Mazoyer 2015) six labels have been modified without regional modification: Cingulum_Ant_L changes to Cingulate_Ant_L Cingulum_Ant_R changes to Cingulate_Ant_R Cingulum_Mid_L changes to Cingulate_Mid_L Cingulum_Mid_R changes to Cingulate_Mid_R Cingulum_Post_L changes to Cingulate_Post_L Cingulum_Post_R changes to Cingulate_Post_R Note 4: aal2 and ROI_MNI_V5 differ only in the index see below. anatomical-name index-aal2 index-ROI_MNI_V5 Precentral_L 1 2001 Precentral_R 2 2002 Frontal_Sup_2_L 3 2101 Frontal_Sup_2_R 4 2102 Frontal_Mid_2_L 5 2201 Frontal_Mid_2_R 6 2202 Frontal_Inf_Oper_L 7 2301 Frontal_Inf_Oper_R 8 2302 Frontal_Inf_Tri_L 9 2311 Frontal_Inf_Tri_R 10 2312 Frontal_Inf_Orb_2_L 11 2321 Frontal_Inf_Orb_2_R 12 2322 Rolandic_Oper_L 13 2331 Rolandic_Oper_R 14 2332 Supp_Motor_Area_L 15 2401 Supp_Motor_Area_R 16 2402 Olfactory_L 17 2501 Olfactory_R 18 2502 Frontal_Sup_Medial_L 19 2601 Frontal_Sup_Medial_R 20 2602 Frontal_Med_Orb_L 21 2611 Frontal_Med_Orb_R 22 2612 Rectus_L 23 2701 Rectus_R 24 2702 OFCmed_L 25 2801 OFCmed_R 26 2802 OFCant_L 27 2811 OFCant_R 28 2812 OFCpost_L 29 2821 OFCpost_R 30 2822 OFClat_L 31 2831 OFClat_R 32 2832 Insula_L 33 3001 Insula_R 34 3002 Cingulate_Ant_L 35 4001 Cingulate_Ant_R 36 4002 Cingulate_Mid_L 37 4011 Cingulate_Mid_R 38 4012 Cingulate_Post_L 39 4021 Cingulate_Post_R 40 4022 Hippocampus_L 41 4101 Hippocampus_R 42 4102 ParaHippocampal_L 43 4111 ParaHippocampal_R 44 4112 Amygdala_L 45 4201 Amygdala_R 46 4202 Calcarine_L 47 5001 Calcarine_R 48 5002 Cuneus_L 49 5011 Cuneus_R 50 5012 Lingual_L 51 5021 Lingual_R 52 5022 Occipital_Sup_L 53 5101 Occipital_Sup_R 54 5102 Occipital_Mid_L 55 5201 Occipital_Mid_R 56 5202 Occipital_Inf_L 57 5301 Occipital_Inf_R 58 5302 Fusiform_L 59 5401 Fusiform_R 60 5402 Postcentral_L 61 6001 Postcentral_R 62 6002 Parietal_Sup_L 63 6101 Parietal_Sup_R 64 6102 Parietal_Inf_L 65 6201 Parietal_Inf_R 66 6202 SupraMarginal_L 67 6211 SupraMarginal_R 68 6212 Angular_L 69 6221 Angular_R 70 6222 Precuneus_L 71 6301 Precuneus_R 72 6302 Paracentral_Lobule_L 73 6401 Paracentral_Lobule_R 74 6402 Caudate_L 75 7001 Caudate_R 76 7002 Putamen_L 77 7011 Putamen_R 78 7012 Pallidum_L 79 7021 Pallidum_R 80 7022 Thalamus_L 81 7101 Thalamus_R 82 7102 Heschl_L 83 8101 Heschl_R 84 8102 Temporal_Sup_L 85 8111 Temporal_Sup_R 86 8112 Temporal_Pole_Sup_L 87 8121 Temporal_Pole_Sup_R 88 8122 Temporal_Mid_L 89 8201 Temporal_Mid_R 90 8202 Temporal_Pole_Mid_L 91 8211 Temporal_Pole_Mid_R 92 8212 Temporal_Inf_L 93 8301 Temporal_Inf_R 94 8302 Cerebelum_Crus1_L 95 9001 Cerebelum_Crus1_R 96 9002 Cerebelum_Crus2_L 97 9011 Cerebelum_Crus2_R 98 9012 Cerebelum_3_L 99 9021 Cerebelum_3_R 100 9022 Cerebelum_4_5_L 101 9031 Cerebelum_4_5_R 102 9032 Cerebelum_6_L 103 9041 Cerebelum_6_R 104 9042 Cerebelum_7b_L 105 9051 Cerebelum_7b_R 106 9052 Cerebelum_8_L 107 9061 Cerebelum_8_R 108 9062 Cerebelum_9_L 109 9071 Cerebelum_9_R 110 9072 Cerebelum_10_L 111 9081 Cerebelum_10_R 112 9082 Vermis_1_2 113 9100 Vermis_3 114 9110 Vermis_4_5 115 9120 Vermis_6 116 9130 Vermis_7 117 9140 Vermis_8 118 9150 Vermis_9 119 9160 Vermis_10 120 9170 > How to install the software 1) Copy the archive to the chosen location (e.g. SPM12 installed in /usr/local/soft) 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/atlas/AAL2.nii /usr/local/soft/spm12/atlas unix> cp /usr/local/soft/spm12/toolbox/aal/atlas/AAL2.xml /usr/local/soft/spm12/atlas 4) To install AAL2 in mricron software (e.g. mricron installed in /usr/local/soft) 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) First option: launch AAL from SPM12: unix> matlab >> 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). 2) Second option: 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 6) Results 6.1) 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 6.2) 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 surrounding the local maxima is fully included in the Postcentral_L region) For each local maximum: -coordinates in mm x,y,z -list of anatomical label and percentage of overlap. Percentage less than 1% is not listed. If part of the region is outside the parcellation the anatomical label will list "OUTSIDE". 6.3) 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 maximum: -coordinates in mm x,y,z of the most significant local maximum of the cluster -list of anatomical label and percentage of overlap. Percentage less than 1% is 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 _ 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. Bibliography Chiavaras MM, Petrides M (2000) Orbitofrontal sulci of the human and macaque monkey brain. J Comp Neurol 422:35-54. Chiavaras MM, LeGoualher G, Evans A, Petrides M (2001) Three-dimensional probabilistic atlas of the human orbitofrontal sulci in standardized stereotaxic space. Neuroimage 13:479-496. Rolls ET, Joliot M, Tzourio-Mazoyer N (2015) Implementation of a new parcellation of the orbitofrontal cortex in the automated anatomical labeling atlas. Neuroimage 10.1016/j.neuroimage.2015.07.075. Tzourio-Mazoyer N, Landeau B, Papathanassiou D, Crivello F, Etard O, Delcroix N, Mazoyer B, Joliot M (2002) Automated anatomical labeling of activations in SPM using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. Neuroimage 15:273-289. History Version vbeta0 Date 01/01/2000 Version vbeta1 Date 01/01/2001 Version vbeta2 Date 26/02/2002 Version vbeta1 Date 17/09/2003 Version v1 Date 14/06/2010 Version v4 Date 25/08/2015 Version v5 Date 25/08/2015 Version v6 Date 03/02/2017 bug fixed for Cluster Labeling option related to the Matlab function called unique on file "gin_det_plabels.m"