add AAL3 atlas

Author: Remi-Gau

atlas/AAL3/AAL3v1.nii.gz

@@ -0,0 +1,167 @@
+label,ROI,hemi
+1,Precentral,L
+2,Precentral,R
+3,Frontal_Sup_2,L
+4,Frontal_Sup_2,R
+5,Frontal_Mid_2,L
+6,Frontal_Mid_2,R
+7,Frontal_Inf_Oper,L
+8,Frontal_Inf_Oper,R
+9,Frontal_Inf_Tri,L
+10,Frontal_Inf_Tri,R
+11,Frontal_Inf_Orb_2,L
+12,Frontal_Inf_Orb_2,R
+13,Rolandic_Oper,L
+14,Rolandic_Oper,R
+15,Supp_Motor_Area,L
+16,Supp_Motor_Area,R
+17,Olfactory,L
+18,Olfactory,R
+19,Frontal_Sup_Medial,L
+20,Frontal_Sup_Medial,R
+21,Frontal_Med_Orb,L
+22,Frontal_Med_Orb,R
+23,Rectus,L
+24,Rectus,R
+25,OFCmed,L
+26,OFCmed,R
+27,OFCant,L
+28,OFCant,R
+29,OFCpost,L
+30,OFCpost,R
+31,OFClat,L
+32,OFClat,R
+33,Insula,L
+34,Insula,R
+37,Cingulate_Mid,L
+38,Cingulate_Mid,R
+39,Cingulate_Post,L
+40,Cingulate_Post,R
+41,Hippocampus,L
+42,Hippocampus,R
+43,ParaHippocampal,L
+44,ParaHippocampal,R
+45,Amygdala,L
+46,Amygdala,R
+47,Calcarine,L
+48,Calcarine,R
+49,Cuneus,L
+50,Cuneus,R
+51,Lingual,L
+52,Lingual,R
+53,Occipital_Sup,L
+54,Occipital_Sup,R
+55,Occipital_Mid,L
+56,Occipital_Mid,R
+57,Occipital_Inf,L
+58,Occipital_Inf,R
+59,Fusiform,L
+60,Fusiform,R
+61,Postcentral,L
+62,Postcentral,R
+63,Parietal_Sup,L
+64,Parietal_Sup,R
+65,Parietal_Inf,L
+66,Parietal_Inf,R
+67,SupraMarginal,L
+68,SupraMarginal,R
+69,Angular,L
+70,Angular,R
+71,Precuneus,L
+72,Precuneus,R
+73,Paracentral,Lobule,L
+74,Paracentral,Lobule,R
+75,Caudate,L
+76,Caudate,R
+77,Putamen,L
+78,Putamen,R
+79,Pallidum,L
+80,Pallidum,R
+83,Heschl,L
+84,Heschl,R
+85,Temporal_Sup,L
+86,Temporal_Sup,R
+87,Temporal_Pole_Sup,L
+88,Temporal_Pole_Sup,R
+89,Temporal_Mid,L
+90,Temporal_Mid,R
+91,Temporal_Pole_Mid,L
+92,Temporal_Pole_Mid,R
+93,Temporal_Inf,L
+94,Temporal_Inf,R
+95,Cerebellum_Crus1,L
+96,Cerebellum_Crus1,R
+97,Cerebellum_Crus2,L
+98,Cerebellum_Crus2,R
+99,Cerebellum_3,L
+100,Cerebellum_3,R
+101,Cerebellum_4_5,L
+102,Cerebellum_4_5,R
+103,Cerebellum_6,L
+104,Cerebellum_6,R
+105,Cerebellum_7b,L
+106,Cerebellum_7b,R
+107,Cerebellum_8,L
+108,Cerebellum_8,R
+109,Cerebellum_9,L
+110,Cerebellum_9,R
+111,Cerebellum_10,L
+112,Cerebellum_10,R
+113,Vermis_1_2
+114,Vermis_3
+115,Vermis_4_5
+116,Vermis_6
+117,Vermis_7
+118,Vermis_8
+119,Vermis_9
+120,Vermis_10
+121,Thal_AV,L
+122,Thal_AV,R
+123,Thal,LP,L
+124,Thal,LP,R
+125,Thal_VA,L
+126,Thal_VA,R
+127,Thal_VL,L
+128,Thal_VL,R
+129,Thal_VPL,L
+130,Thal_VPL,R
+131,Thal_IL,L
+132,Thal_IL,R
+133,Thal,Re,L
+134,Thal,Re,R
+135,Thal_MDm,L
+136,Thal_MDm,R
+137,Thal_MDl,L
+138,Thal_MDl,R
+139,Thal,LGN,L
+140,Thal,LGN,R
+141,Thal_MGN,L
+142,Thal_MGN,R
+143,Thal_PuI,L
+144,Thal_PuI,R
+145,Thal_PuM,L
+146,Thal_PuM,R
+147,Thal_PuA,L
+148,Thal_PuA,R
+149,Thal_PuL,L
+150,Thal_PuL,R
+151,ACC_sub,L
+152,ACC_sub,R
+153,ACC_pre,L
+154,ACC_pre,R
+155,ACC_sup,L
+156,ACC_sup,R
+157,N_Acc,L
+158,N_Acc,R
+159,VTA,L
+160,VTA,R
+161,SN_pc,L
+162,SN_pc,R
+163,SN_pr,L
+164,SN_pr,R
+165,Red_N,L
+166,Red_N,R
+167,LC,L
+168,LC,R
+169,Raphe_D,n/a
+170,Raphe_M,n/a

atlas/AAL3/AAL3v1_1mm.nii.gz

@@ -0,0 +1,54 @@
+function copyAtlasToSpmDir(atlas)
+  %
+  % copies a given atlas to the SPM atlas dir
+  %
+  % USAGE::
+  %
+  %   copyAtlasToSpmDir(atlas)
+  %
+  % :param atlas: Any of ``{'AAL'}``. Defaults to ``'AAL'``
+  % :type  atlas: char
+  %
+  % (C) Copyright 2022 CPP_SPM developers
+  
+  if nargin < 1
+    atlas = 'AAL';
+  end
+  
+  spmAtlasDir = fullfile(spm('dir'), 'atlas');
+  cppRoiAtlasDir = returnAtlasDir();
+  
+  switch lower(atlas)
+    
+    case 'aal'
+      sourceAtlasImage = fullfile(cppRoiAtlasDir, 'AAL3', 'AAL3v1_1mm.nii.gz');
+      sourceAtlasXml = fullfile(cppRoiAtlasDir, 'AAL3', 'AAL3v1_1mm.xml');
+  end
+  
+  targetAtlasImage = fullfile(spmAtlasDir, spm_file(sourceAtlasImage, 'filename'));
+  targetAtlasXml = fullfile(spmAtlasDir, spm_file(sourceAtlasXml, 'filename'));
+  
+  atlasPresent = isdir(spmAtlasDir) && ...
+                 exist(targetAtlasImage(1:end-3), 'file') && ...
+                 exist(targetAtlasXml, 'file');
+  
+  if ~atlasPresent
+    fprintf('\nCopying atlas "%s" to spm atlas directory:\n\t%s\n', ...
+            atlas, ...
+            spmAtlasDir)
+    spm_mkdir(spmAtlasDir);
+    
+    copyfile(sourceAtlasImage, spmAtlasDir);
+    gunzip(fullfile(spmAtlasDir, '*.nii.gz'))
+    delete(fullfile(spmAtlasDir, '*.nii.gz'))
+    
+    copyfile(sourceAtlasXml, spmAtlasDir);
+    
+  else
+    fprintf('\nAtlas "%s" already in spm atlas directory:\n\t%s\n', ...
+      atlas, ...
+      spmAtlasDir)
+    
+  end
+  
+end