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vb_atlas2vb_std_aal

PURPOSE ^

vb_atlas2vb create an areafile based on the anatomical atlas

SYNOPSIS ^

function vb_atlas2vb_std_aal(parm)

DESCRIPTION ^

 vb_atlas2vb create an areafile based on the anatomical atlas
 
 ---- Syntax
 vb_atlas2vb_std_aal(parm)

 ---- Input (Field names in 'parm')
 atlas_id   : ID of atlas.
 atlas_text : atlas label name text file 
 atlas_file : atlas image file 
 save_areafile  : Area file saved
 save_atlasfile : Atlas file saved
 brainfile      : brain file;

 --- Function required  
  explode      : string manupilation 

 ---- NOTE -----
 When using the normalize transformation matrix created by 'spm99',  
 back transformation results with a little shift 
 toward X(Left-Right) direction compared with brain file.
 It is highly recommended to recalculate 
 the transformation matrix by spm2 !!!

 2005/03/03 OY
 2005/03/28 modified 
 2005/04/21 second part modified
 2005/09/09 ver.030b compatible
 2005/12/22 M.Sato
 2006/2/3   M.Sato
 2006/11/14 M.Sato
 2007/03/05 OY
 * MNI coordinate is stored in brainfile.
 * save_xyzfile is removed.
 * A label for 'Corpus' is NaN.
 2009-01-05 Taku Yoshioka
   Supression of confirmation dialog

 Copyright (C) 2011, ATR All Rights Reserved.
 License : New BSD License(see VBMEG_LICENSE.txt)

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function    vb_atlas2vb_std_aal(parm)
0002 % vb_atlas2vb create an areafile based on the anatomical atlas
0003 %
0004 % ---- Syntax
0005 % vb_atlas2vb_std_aal(parm)
0006 %
0007 % ---- Input (Field names in 'parm')
0008 % atlas_id   : ID of atlas.
0009 % atlas_text : atlas label name text file
0010 % atlas_file : atlas image file
0011 % save_areafile  : Area file saved
0012 % save_atlasfile : Atlas file saved
0013 % brainfile      : brain file;
0014 %
0015 % --- Function required
0016 %  explode      : string manupilation
0017 %
0018 % ---- NOTE -----
0019 % When using the normalize transformation matrix created by 'spm99',
0020 % back transformation results with a little shift
0021 % toward X(Left-Right) direction compared with brain file.
0022 % It is highly recommended to recalculate
0023 % the transformation matrix by spm2 !!!
0024 %
0025 % 2005/03/03 OY
0026 % 2005/03/28 modified
0027 % 2005/04/21 second part modified
0028 % 2005/09/09 ver.030b compatible
0029 % 2005/12/22 M.Sato
0030 % 2006/2/3   M.Sato
0031 % 2006/11/14 M.Sato
0032 % 2007/03/05 OY
0033 % * MNI coordinate is stored in brainfile.
0034 % * save_xyzfile is removed.
0035 % * A label for 'Corpus' is NaN.
0036 % 2009-01-05 Taku Yoshioka
0037 %   Supression of confirmation dialog
0038 %
0039 % Copyright (C) 2011, ATR All Rights Reserved.
0040 % License : New BSD License(see VBMEG_LICENSE.txt)
0041 
0042 %
0043 % ---- Define aal-atlas
0044 %
0045 
0046 % Max value corresponding to Cerebrum cortex region in aal-atlas
0047 %  1-90: Cerebrum, 91-108: Cerebellum, 109-116: Vermis
0048 MaxLabel   = 90;    
0049 
0050 atlas_dir  = parm.atlas_dir;
0051 atlas_id   = 'aal';
0052 atlas_text = [atlas_dir 'aal.txt'];
0053 atlas_file = [atlas_dir 'aal.img'];
0054 
0055 brainfile  = parm.brainfile;
0056 
0057 save_areafile  = parm.save_areafile;
0058 save_atlasfile = parm.save_atlasfile;
0059 
0060 % In the 1st-step, nearest point is searched within Rmax
0061 % In the 2nd-step, nearest point is searched for all candidates
0062 % This value determine, efficiency of search,
0063 % but does not change the result
0064 
0065 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0066 %%%%%%%%%%%%%%%%%%%% Don't modify %%%%%%%%%%%%%%%%%%%%%%%%%%%
0067 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0068 
0069 %%% Template file is neurological format (right handed spm).
0070 
0071 % Standard brain cortex in MNI-mm coordinate (origin in MNI-space)
0072 load(brainfile,'V','F')
0073 
0074 NL = F.NdipoleL;
0075 NP = size(V,1);
0076 Vlabel     = zeros(NP,1);
0077 
0078 % Read atlas-template image
0079 % Zlabel - label for 3D image data (label value)
0080 % XYZmm0 - 3 x n matrix of XYZ locations
0081 %          mm-coordinates in atlas-template (origin : AC-PC center)
0082 
0083 avw = avw_img_read(atlas_file);
0084 Zlabel = avw.img;
0085 
0086 % Read image-header
0087 [dim, Trans] = vb_get_image_info(atlas_file);
0088 
0089 % convert to standard voxcel coordinate from mm-coordinate
0090 Vox = [V*1000 ones(NP,1)] * inv(Trans');
0091 Vox = round(Vox(:,1:3));
0092 
0093 % Extract labeled left/right region
0094 mni_L = sub2ind(dim, ...
0095         Vox(1:NL,1),Vox(1:NL,2),Vox(1:NL,3));
0096 mni_R = sub2ind(dim, ...
0097         Vox(1+NL:end,1),Vox(1+NL:end,2),Vox(1+NL:end,3));
0098 
0099 %
0100 % ---- Left brain (Left label is odd integer in 'aal')
0101 %
0102 label_L = Zlabel(mni_L);
0103 ixz  = find( mod( label_L, 2 ) == 0 | label_L > MaxLabel);
0104 label_L(ixz) = 0;
0105 %
0106 % ---- Right brain (Right label is even integer in 'aal')
0107 %
0108 label_R = Zlabel(mni_R);
0109 ixz  = find( mod( label_R, 2 ) == 1 | label_R > MaxLabel);
0110 label_R(ixz) = 0;
0111 
0112 fprintf('--- Mapping Atlas-label onto 2D cortical surface \n');
0113 
0114 %
0115 % ---- Save labeled area
0116 %
0117 Nlabel_L = sum( label_L ~= 0 );    % # of labeled points
0118 Nlabel_R = sum( label_R ~= 0 );    % # of labeled points
0119 
0120 fprintf('# of all vertex     = %d\n',NP)
0121 fprintf('# of labeled points = %d\n',Nlabel_L+Nlabel_R)
0122 
0123 % Read atlas text file and extract area keys.
0124 [label, label_name] = vb_read_atlas_label(atlas_text);
0125 
0126 % Save area label into area file
0127 fprintf('Save the area file as "%s" \n', save_areafile);
0128 
0129 Vlabel(1:NL) = label_L;
0130 Vlabel(1+NL:end) = label_R;
0131 
0132 vb_save_atlas_label(save_areafile,Vlabel,label,label_name);
0133 
0134 % Intensity of 'Act.xxP' is the label for each vertex
0135 Atlas.key = [atlas_id];
0136 Atlas.xxP = Vlabel;
0137 Atlas.label      = label;
0138 Atlas.label_name = label_name;
0139 
0140 % Save label as actfile
0141 fprintf('Save the atlas file as "%s"  \n', save_atlasfile);
0142 vb_add_act(save_atlasfile,Atlas,[],false);
0143 
0144 
0145 %clear Zlabel Vlabel XYZmm0 XYZmm Zlabel

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