select_slice

 select slice from 3D image
  [B3, Xdim, Ydim] = select_slice(B,indx,vdim)

 B : 3D-image [NBx, NBy, NBz]. The coordinate system must be RAS. 
     Note that the default of ANALYZE coordinate is LAS. 
 indx : slice index in vdim-axis
 vdim : slice cut direction
      = 'x' : Sagittal cut : Y-Z plane
      = 'y' : Coronal cut : X-Z plane
      = 'z' : Transverse (Axial) cut : X-Y plane
  B3        selected 2D slice image
  Xdim     
  Ydim     

      image(Xdim, Ydim, B3, 'CDataMapping','scaled');

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

0001 function    [B3, Xdim, Ydim] = select_slice(B,indx,vdim)
0002 % select slice from 3D image
0003 %  [B3, Xdim, Ydim] = select_slice(B,indx,vdim)
0004 %
0005 % B : 3D-image [NBx, NBy, NBz]. The coordinate system must be RAS.
0006 %     Note that the default of ANALYZE coordinate is LAS.
0007 % indx : slice index in vdim-axis
0008 % vdim : slice cut direction
0009 %      = 'x' : Sagittal cut : Y-Z plane
0010 %      = 'y' : Coronal cut : X-Z plane
0011 %      = 'z' : Transverse (Axial) cut : X-Y plane
0012 %  B3        selected 2D slice image
0013 %  Xdim
0014 %  Ydim
0015 %
0016 %      image(Xdim, Ydim, B3, 'CDataMapping','scaled');
0017 %
0018 % Copyright (C) 2011, ATR All Rights Reserved.
0019 % License : New BSD License(see VBMEG_LICENSE.txt)
0020 
0021 
0022 indx = round(indx);
0023 
0024 [NBx,NBy,NBz]=size(B);
0025 
0026 % dimension of image data
0027 xdim = [0, NBx];
0028 ydim = [0, NBy];
0029 zdim = [0, NBz];
0030 
0031 % Analyze-slice-cut direction
0032 switch    vdim,
0033 case    'x',
0034      % 'SAG' : Sagittal cut : Y-Z plane
0035      B2   = reshape(B(indx,:,:),NBy,NBz);
0036      Xdim = ydim;
0037      Ydim = zdim;
0038 case    'y',
0039      % 'COR' : Coronal cut : X-Z plane
0040      B2   = reshape(B(:,indx,:),NBx,NBz);
0041      Xdim = xdim;
0042      Ydim = zdim;
0043 case    'z',
0044      % 'TRN' : Transverse (Axial) cut : X-Y plane
0045      B2   = B(:,:,indx);
0046      Xdim = xdim;
0047      Ydim = ydim;
0048 end;
0049 
0050 % Squeeze to 2D
0051 B2 = squeeze(B2); 
0052 
0053 % RGB color matrix (gray level): transpose of 2D matrix for image plot
0054 B3 = repmat(B2',[1 1 3]);
0055 
0056 return
0057 %%%%%%%%%%%%%--------------------END-----------------
0058 
0059 [Nx,Ny] = size(B2);
0060 
0061 % Index color -> True color
0062 if nargin < 4
0063     B3 = repmat(B2,[1 1 3]);
0064     
0065     image(Xdim, Ydim, B3, 'CDataMapping','scaled');
0066 else
0067     BC = zeros(Nx,Ny,3);
0068     BC(:,:,cdim) = B2;
0069 %
0070 %    sum(BC(:) > 0)
0071     
0072     image(Xdim, Ydim, BC, 'CDataMapping','scaled');
0073 end
0074 
0075 set(gca,'YDir','normal','XLimMode','manual','YLimMode','manual');
0076 axis equal
0077 axis tight